6R5Q image
Deposition Date 2019-03-25
Release Date 2019-07-10
Last Version Date 2024-11-20
Entry Detail
PDB ID:
6R5Q
Keywords:
Title:
Structure of XBP1u-paused ribosome nascent chain complex (post-state)
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.00 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:eS31
Gene (Uniprot):RPS27A
Chain IDs:EC (auth: 0)
Chain Length:68
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:X-box-binding protein 1
Gene (Uniprot):XBP1
Chain IDs:B (auth: 1)
Chain Length:24
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:P-tRNA
Chain IDs:C (auth: 2)
Chain Length:76
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:E-tRNA
Chain IDs:A (auth: 3)
Chain Length:75
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:DC (auth: 4)
Chain Length:6
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:28S ribosomal RNA
Chain IDs:D (auth: 5)
Chain Length:3543
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:ribosomal protein RACK1
Gene (Uniprot):RACK1
Chain IDs:FC (auth: 6)
Chain Length:313
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:E (auth: 7)
Chain Length:120
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polyribonucleotide
Molecule:5.8S ribosomal RNA
Chain IDs:F (auth: 8)
Chain Length:151
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:uS14
Gene (Uniprot):RPS29
Chain IDs:CC (auth: 9)
Chain Length:55
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:uL2
Gene (Uniprot):RPL8
Chain IDs:G (auth: A)
Chain Length:248
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S30
Gene (Uniprot):FAU
Chain IDs:GC (auth: AA)
Chain Length:55
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:uL3
Gene (Uniprot):RPL3
Chain IDs:H (auth: B)
Chain Length:104
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7
Gene (Uniprot):RPS7
Chain IDs:GB (auth: BB)
Chain Length:189
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:uL4
Gene (Uniprot):RPL4
Chain IDs:I (auth: C)
Chain Length:98
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8
Gene (Uniprot):RPS8
Chain IDs:HB (auth: CC)
Chain Length:206
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L5
Chain IDs:J (auth: D)
Chain Length:293
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S9 (Predicted)
Gene (Uniprot):RPS9
Chain IDs:IB (auth: DD)
Chain Length:185
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6
Gene (Uniprot):RPL6
Chain IDs:K (auth: E)
Chain Length:128
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S11
Gene (Uniprot):RPS11
Chain IDs:KB (auth: EE)
Chain Length:151
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:uL30
Gene (Uniprot):RPL7
Chain IDs:L (auth: F)
Chain Length:225
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S28
Gene (Uniprot):RPS28
Chain IDs:BC (auth: FF)
Chain Length:62
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:eL8
Gene (Uniprot):RPL7A
Chain IDs:M (auth: G)
Chain Length:233
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:uS10
Chain IDs:TB (auth: GG)
Chain Length:100
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:uL6
Chain IDs:N (auth: H)
Chain Length:190
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:eS21
Chain IDs:UB (auth: HH)
Chain Length:83
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L10 (Predicted)
Gene (Uniprot):RPL10
Chain IDs:O (auth: I)
Chain Length:205
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:uS13
Chain IDs:RB (auth: II)
Chain Length:144
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L11
Gene (Uniprot):RPL11
Chain IDs:P (auth: J)
Chain Length:170
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27
Gene (Uniprot):RPS27
Chain IDs:AC (auth: JJ)
Chain Length:83
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polyribonucleotide
Molecule:18S ribosomal RNA
Chain IDs:YA (auth: K)
Chain Length:1698
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:eS17
Gene (Uniprot):RPS17
Chain IDs:QB (auth: KK)
Chain Length:132
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13
Chain IDs:Q (auth: L)
Chain Length:210
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:eS26
Chain IDs:ZB (auth: LL)
Chain Length:101
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L14
Chain IDs:R (auth: M)
Chain Length:138
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:uS11
Gene (Uniprot):RPS14
Chain IDs:NB (auth: MM)
Chain Length:135
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L15
Gene (Uniprot):RPL15
Chain IDs:S (auth: N)
Chain Length:25
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:eS24
Chain IDs:XB (auth: NN)
Chain Length:124
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:uL13
Chain IDs:T (auth: O)
Chain Length:104
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eS25
Gene (Uniprot):RPS25
Chain IDs:YB (auth: OO)
Chain Length:75
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:uL22
Chain IDs:U (auth: P)
Chain Length:153
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:eS19
Gene (Uniprot):RPS19
Chain IDs:SB (auth: PP)
Chain Length:141
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:eL18
Chain IDs:V (auth: Q)
Chain Length:187
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:ribosomal protein uS15
Gene (Uniprot):RPS13
Chain IDs:MB (auth: QQ)
Chain Length:149
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:eL19
Chain IDs:W (auth: R)
Chain Length:180
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S12
Gene (Uniprot):RPS12
Chain IDs:LB (auth: RR)
Chain Length:117
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:eL20
Chain IDs:X (auth: S)
Chain Length:196
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:eS10
Chain IDs:JB (auth: SS)
Chain Length:96
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:eL21
Gene (Uniprot):RPL21
Chain IDs:Y (auth: T)
Chain Length:159
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S15a
Gene (Uniprot):RPS15A
Chain IDs:VB (auth: TT)
Chain Length:129
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:eL22
Chain IDs:Z (auth: U)
Chain Length:213
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S16
Gene (Uniprot):RPS16
Chain IDs:PB (auth: UU)
Chain Length:142
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:eL14
Gene (Uniprot):RPL23
Chain IDs:AA (auth: V)
Chain Length:131
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S23
Gene (Uniprot):RPS23
Chain IDs:WB (auth: VV)
Chain Length:141
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L24
Gene (Uniprot):RPL24
Chain IDs:BA (auth: W)
Chain Length:121
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:uS17
Gene (Uniprot):RPS15
Chain IDs:OB (auth: WW)
Chain Length:120
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:uL23
Gene (Uniprot):RPL23A
Chain IDs:CA (auth: X)
Chain Length:118
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L26
Gene (Uniprot):RPL26
Chain IDs:DA (auth: Y)
Chain Length:191
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27
Gene (Uniprot):RPL27
Chain IDs:EA (auth: Z)
Chain Length:135
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:uL15
Gene (Uniprot):RPL27A
Chain IDs:FA (auth: a)
Chain Length:248
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:eL29
Gene (Uniprot):RPL29
Chain IDs:GA (auth: b)
Chain Length:104
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:eL30
Gene (Uniprot):RPL30
Chain IDs:HA (auth: c)
Chain Length:98
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:eL31
Gene (Uniprot):RPL31
Chain IDs:IA (auth: d)
Chain Length:293
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:eL32
Gene (Uniprot):RPL32
Chain IDs:JA (auth: e)
Chain Length:128
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:eL33
Gene (Uniprot):RPL35A
Chain IDs:KA (auth: f)
Chain Length:225
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:eL34
Chain IDs:LA (auth: g)
Chain Length:233
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:uL29
Gene (Uniprot):RPL35
Chain IDs:MA (auth: h)
Chain Length:190
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36
Gene (Uniprot):RPL36
Chain IDs:NA (auth: i)
Chain Length:205
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L37
Gene (Uniprot):RPL37
Chain IDs:OA (auth: j)
Chain Length:170
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:eL38
Chain IDs:PA (auth: k)
Chain Length:1698
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:eL39
Gene (Uniprot):LOC100343258
Chain IDs:QA (auth: l)
Chain Length:210
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:eL40
Chain IDs:RA (auth: m)
Chain Length:138
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60s ribosomal protein l41
Gene (Uniprot):RPL41
Chain IDs:SA (auth: n)
Chain Length:25
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:eL42
Gene (Uniprot):RPL36A
Chain IDs:TA (auth: o)
Chain Length:104
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:ribosomal protein eL43
Gene (Uniprot):RPL37A
Chain IDs:UA (auth: p)
Chain Length:153
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:uS2
Chain IDs:ZA (auth: q)
Chain Length:187
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:eL28
Gene (Uniprot):RPL28
Chain IDs:VA (auth: r)
Chain Length:180
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S acidic ribosomal protein P0
Chain IDs:WA (auth: s)
Chain Length:196
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:uL11
Gene (Uniprot):RPL12
Chain IDs:XA (auth: t)
Chain Length:159
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3a
Gene (Uniprot):RPS3A
Chain IDs:AB (auth: u)
Chain Length:213
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:uS5
Chain IDs:BB (auth: v)
Chain Length:131
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S3
Gene (Uniprot):RPS3
Chain IDs:CB (auth: w)
Chain Length:121
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4
Gene (Uniprot):RPS4X
Chain IDs:DB (auth: x)
Chain Length:118
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S5
Gene (Uniprot):RPS5
Chain IDs:EB (auth: y)
Chain Length:191
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6
Gene (Uniprot):RPS6
Chain IDs:FB (auth: z)
Chain Length:135
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Primary Citation
Structural and mutational analysis of the ribosome-arresting human XBP1u.
Elife 8 ? ? (2019)
PMID: 31246176 DOI: 10.7554/eLife.46267

Abstact

XBP1u, a central component of the unfolded protein response (UPR), is a mammalian protein containing a functionally critical translational arrest peptide (AP). Here, we present a 3 Å cryo-EM structure of the stalled human XBP1u AP. It forms a unique turn in the ribosomal exit tunnel proximal to the peptidyl transferase center where it causes a subtle distortion, thereby explaining the temporary translational arrest induced by XBP1u. During ribosomal pausing the hydrophobic region 2 (HR2) of XBP1u is recognized by SRP, but fails to efficiently gate the Sec61 translocon. An exhaustive mutagenesis scan of the XBP1u AP revealed that only 8 out of 20 mutagenized positions are optimal; in the remaining 12 positions, we identify 55 different mutations increase the level of translational arrest. Thus, the wildtype XBP1u AP induces only an intermediate level of translational arrest, allowing efficient targeting by SRP without activating the Sec61 channel.

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Protein

Chemical

Disease

Primary Citation of related structures