ISDA: 4V4G

Deposition Date 2004-10-06

Release Date 2014-07-09

Last Version Date 2024-11-20

Entry Detail

PDB ID:

4V4G

Keywords:

RIBOSOME

Title:

Crystal structure of five 70s ribosomes from Escherichia Coli in complex with protein Y.

Biological Source:

Source Organism:

Escherichia coli (Taxon ID: 562)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

11.50 Å

R-Value Free:

0.40

R-Value Work:

0.39

R-Value Observed:

0.39

Space Group:

I 4 2 2

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:A (auth: AA), BB (auth: CA), CD (auth: EA), DF (auth: GA), EH (auth: IA)
Chain Length:90
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Chain IDs:B (auth: AB), CB, DD (auth: EB), EF (auth: GB), FH (auth: IB)
Chain Length:234
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Chain IDs:C (auth: AC), DB (auth: CC), ED (auth: EC), FF (auth: GC), GH (auth: IC)
Chain Length:206
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Chain IDs:D (auth: AD), EB (auth: CD), FD (auth: ED), GF (auth: GD), HH (auth: ID)
Chain Length:208
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Chain IDs:E (auth: AE), FB (auth: CE), GD (auth: EE), HF (auth: GE), IH (auth: IE)
Chain Length:150
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Chain IDs:F (auth: AF), GB (auth: CF), HD (auth: EF), IF (auth: GF), JH (auth: IF)
Chain Length:101
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Chain IDs:G (auth: AG), HB (auth: CG), ID (auth: EG), JF (auth: GG), KH (auth: IG)
Chain Length:155
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Chain IDs:H (auth: AH), IB (auth: CH), JD (auth: EH), KF (auth: GH), LH (auth: IH)
Chain Length:138
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Chain IDs:I (auth: AI), JB (auth: CI), KD (auth: EI), LF (auth: GI), MH (auth: II)
Chain Length:127
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Chain IDs:J (auth: AJ), KB (auth: CJ), LD (auth: EJ), MF (auth: GJ), NH (auth: IJ)
Chain Length:98
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Chain IDs:K (auth: AK), LB (auth: CK), MD (auth: EK), NF (auth: GK), OH (auth: IK)
Chain Length:119
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Chain IDs:L (auth: AL), MB (auth: CL), ND (auth: EL), OF (auth: GL), PH (auth: IL)
Chain Length:124
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Chain IDs:M (auth: AM), NB (auth: CM), OD (auth: EM), PF (auth: GM), QH (auth: IM)
Chain Length:125
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Chain IDs:N (auth: AN), OB (auth: CN), PD (auth: EN), QF (auth: GN), RH (auth: IN)
Chain Length:60
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Chain IDs:O (auth: AO), PB (auth: CO), QD (auth: EO), RF (auth: GO), SH (auth: IO)
Chain Length:88
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Chain IDs:P (auth: AP), QB (auth: CP), RD (auth: EP), SF (auth: GP), TH (auth: IP)
Chain Length:83
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Chain IDs:Q (auth: AQ), RB (auth: CQ), SD (auth: EQ), TF (auth: GQ), UH (auth: IQ)
Chain Length:104
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Chain IDs:R (auth: AR), SB (auth: CR), TD (auth: ER), UF (auth: GR), VH (auth: IR)
Chain Length:73
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Chain IDs:S (auth: AS), TB (auth: CS), UD (auth: ES), VF (auth: GS), WH (auth: IS)
Chain Length:80
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Chain IDs:T (auth: AT), UB (auth: CT), VD (auth: ET), WF (auth: GT), XH (auth: IT)
Chain Length:99
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:protein Y
Chain IDs:U (auth: Aa), VB (auth: Ca), WD (auth: Ea), XF (auth: Ga), YH (auth: Ia)
Chain Length:90
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Chain IDs:UA (auth: B1), VC (auth: D1), WE (auth: F1), XG (auth: H1), YI (auth: J1)
Chain Length:73
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Chain IDs:VA (auth: B2), WC (auth: D2), XE (auth: F2), YG (auth: H2), ZI (auth: J2)
Chain Length:58
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Chain IDs:WA (auth: B3), XC (auth: D3), YE (auth: F3), ZG (auth: H3), AJ (auth: J3)
Chain Length:53
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Chain IDs:XA (auth: B4), YC (auth: D4), ZE (auth: F4), AH (auth: H4), BJ (auth: J4)
Chain Length:46
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Chain IDs:YA (auth: B5), ZC (auth: D5), AF (auth: F5), BH (auth: H5), CJ (auth: J5)
Chain Length:63
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Chain IDs:ZA (auth: B6), AD (auth: D6), BF (auth: F6), CH (auth: H6), DJ (auth: J6)
Chain Length:35
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L1P
Chain IDs:AB (auth: B7), BD (auth: D7), CF (auth: F7), DH (auth: H7), EJ (auth: J7)
Chain Length:217
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polyribonucleotide
Molecule:5S RIBOSOMAL RNA
Chain IDs:W (auth: BA), XB (auth: DA), YD (auth: FA), ZF (auth: HA), AI (auth: JA)
Chain Length:119
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polyribonucleotide
Molecule:23S RIBOSOMAL RNA
Chain IDs:V (auth: BB), WB (auth: DB), XD (auth: FB), YF (auth: HB), ZH (auth: JB)
Chain Length:2825
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Chain IDs:X (auth: BD), YB (auth: DD), ZD (auth: FD), AG (auth: HD), BI (auth: JD)
Chain Length:270
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Chain IDs:Y (auth: BE), ZB (auth: DE), AE (auth: FE), BG (auth: HE), CI (auth: JE)
Chain Length:205
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Chain IDs:Z (auth: BF), AC (auth: DF), BE (auth: FF), CG (auth: HF), DI (auth: JF)
Chain Length:198
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Chain IDs:AA (auth: BG), BC (auth: DG), CE (auth: FG), DG (auth: HG), EI (auth: JG)
Chain Length:178
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Chain IDs:BA (auth: BH), CC (auth: DH), DE (auth: FH), EG (auth: HH), FI (auth: JH)
Chain Length:177
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Chain IDs:CA (auth: BI), DC (auth: DI), EE (auth: FI), FG (auth: HI), GI (auth: JI)
Chain Length:52
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Chain IDs:DA (auth: BJ), EC (auth: DJ), FE (auth: FJ), GG (auth: HJ), HI (auth: JJ)
Chain Length:143
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Chain IDs:EA (auth: BK), FC (auth: DK), GE (auth: FK), HG (auth: HK), II (auth: JK)
Chain Length:143
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Chain IDs:FA (auth: BL), GC (auth: DL), HE (auth: FL), IG (auth: HL), JI (auth: JL)
Chain Length:132
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Chain IDs:GA (auth: BM), HC (auth: DM), IE (auth: FM), JG (auth: HM), KI (auth: JM)
Chain Length:141
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Chain IDs:HA (auth: BN), IC (auth: DN), JE (auth: FN), KG (auth: HN), LI (auth: JN)
Chain Length:124
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Chain IDs:IA (auth: BO), JC (auth: DO), KE (auth: FO), LG (auth: HO), MI (auth: JO)
Chain Length:114
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Chain IDs:JA (auth: BP), KC (auth: DP), LE (auth: FP), MG (auth: HP), NI (auth: JP)
Chain Length:111
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Chain IDs:KA (auth: BQ), LC (auth: DQ), ME (auth: FQ), NG (auth: HQ), OI (auth: JQ)
Chain Length:125
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Chain IDs:LA (auth: BR), MC (auth: DR), NE (auth: FR), OG (auth: HR), PI (auth: JR)
Chain Length:117
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Chain IDs:MA (auth: BS), NC (auth: DS), OE (auth: FS), PG (auth: HS), QI (auth: JS)
Chain Length:100
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Chain IDs:NA (auth: BT), OC (auth: DT), PE (auth: FT), QG (auth: HT), RI (auth: JT)
Chain Length:130
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Chain IDs:OA (auth: BU), PC (auth: DU), QE (auth: FU), RG (auth: HU), SI (auth: JU)
Chain Length:93
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Chain IDs:PA (auth: BV), QC (auth: DV), RE (auth: FV), SG (auth: HV), TI (auth: JV)
Chain Length:113
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:general stress protein Ctc
Chain IDs:QA (auth: BW), RC (auth: DW), SE (auth: FW), TG (auth: HW), UI (auth: JW)
Chain Length:173
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Chain IDs:RA (auth: BX), SC (auth: DX), TE (auth: FX), UG (auth: HX), VI (auth: JX)
Chain Length:86
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Chain IDs:SA (auth: BY), TC (auth: DY), UE (auth: FY), VG (auth: HY), WI (auth: JY)
Chain Length:65
Number of Molecules:5
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Chain IDs:TA (auth: BZ), UC (auth: DZ), VE (auth: FZ), WG (auth: HZ), XI (auth: JZ)
Chain Length:55
Number of Molecules:5
Biological Source:Escherichia coli

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
MSE	AB	MET	SELENOMETHIONINE

Ligand Molecules

Primary Citation

Structural basis for the control of translation initiation during stress.

Vila-Sanjurjo, A, Schuwirth, B.S, Hau, C.W, Cate, J.H.Show

Nat.Struct.Mol.Biol. 11 1054 1059 (2004)

PMID: 15502846 DOI: 10.1038/nsmb850

Abstact

During environmental stress, organisms limit protein synthesis by storing inactive ribosomes that are rapidly reactivated when conditions improve. Here we present structural and biochemical data showing that protein Y, an Escherichia coli stress protein, fills the tRNA- and mRNA-binding channel of the small ribosomal subunit to stabilize intact ribosomes. Protein Y inhibits translation initiation during cold shock but not at normal temperatures. Furthermore, protein Y competes with conserved translation initiation factors that, in bacteria, are required for ribosomal subunit dissociation. The mechanism used by protein Y to reduce translation initiation during stress and quickly release ribosomes for renewed translation initiation may therefore occur widely in nature.

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Disease

Primary Citation of related structures

Abstact

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