5VYC image
Deposition Date 2017-05-24
Release Date 2017-07-19
Last Version Date 2024-12-25
Entry Detail
PDB ID:
5VYC
Keywords:
Title:
Crystal structure of the human 40S ribosomal subunit in complex with DENR-MCT-1.
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
6.00 Å
R-Value Free:
0.32
R-Value Work:
0.32
R-Value Observed:
0.32
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein SA
Gene (Uniprot):RPSA
Chain IDs:V (auth: A1), EB (auth: A2), NC (auth: A3), WD (auth: A4), FF (auth: A5), OG (auth: A6)
Chain Length:115
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3a
Gene (Uniprot):RPS3A
Chain IDs:W (auth: B1), FB (auth: B2), OC (auth: B3), XD (auth: B4), GF (auth: B5), PG (auth: B6)
Chain Length:264
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S2
Gene (Uniprot):RPS2
Chain IDs:J (auth: C1), SA (auth: C2), BC (auth: C3), KD (auth: C4), TE (auth: C5), CG (auth: C6)
Chain Length:293
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3
Gene (Uniprot):RPS3
Chain IDs:X (auth: D1), GB (auth: D2), PC (auth: D3), YD (auth: D4), HF (auth: D5), QG (auth: D6)
Chain Length:56
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4, X isoform
Gene (Uniprot):RPS4X
Chain IDs:Y (auth: E1), HB (auth: E2), QC (auth: E3), ZD (auth: E4), IF (auth: E5), RG (auth: E6)
Chain Length:263
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S5
Gene (Uniprot):RPS5
Chain IDs:Z (auth: F1), IB (auth: F2), RC (auth: F3), AE (auth: F4), JF (auth: F5), SG (auth: F6)
Chain Length:204
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6
Gene (Uniprot):RPS6
Chain IDs:K (auth: G1), TA (auth: G2), CC (auth: G3), LD (auth: G4), UE (auth: G5), DG (auth: G6)
Chain Length:317
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7
Gene (Uniprot):RPS7
Chain IDs:AA (auth: H1), JB (auth: H2), SC (auth: H3), BE (auth: H4), KF (auth: H5), TG (auth: H6)
Chain Length:194
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8
Gene (Uniprot):RPS8
Chain IDs:BA (auth: I1), KB (auth: I2), TC (auth: I3), CE (auth: I4), LF (auth: I5), UG (auth: I6)
Chain Length:1869
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S9
Gene (Uniprot):RPS9
Chain IDs:L (auth: J1), UA (auth: J2), DC (auth: J3), MD (auth: J4), VE (auth: J5), EG (auth: J6)
Chain Length:194
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S10
Gene (Uniprot):RPS10
Chain IDs:CA (auth: K1), LB (auth: K2), UC (auth: K3), DE (auth: K4), MF (auth: K5), VG (auth: K6)
Chain Length:181
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S11
Gene (Uniprot):RPS11
Chain IDs:DA (auth: L1), MB (auth: L2), VC (auth: L3), EE (auth: L4), NF (auth: L5), WG (auth: L6)
Chain Length:198
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S12
Gene (Uniprot):RPS12
Chain IDs:M (auth: M1), VA (auth: M2), EC (auth: M3), ND (auth: M4), WE (auth: M5), FG (auth: M6)
Chain Length:132
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S13
Gene (Uniprot):RPS13
Chain IDs:N (auth: N1), WA (auth: N2), FC (auth: N3), OD (auth: N4), XE (auth: N5), GG (auth: N6)
Chain Length:151
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S14
Gene (Uniprot):RPS14
Chain IDs:O (auth: O1), XA (auth: O2), GC (auth: O3), PD (auth: O4), YE (auth: O5), HG (auth: O6)
Chain Length:151
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15
Gene (Uniprot):RPS15
Chain IDs:EA (auth: P1), NB (auth: P2), WC (auth: P3), FE (auth: P4), OF (auth: P5), XG (auth: P6)
Chain Length:145
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S16
Gene (Uniprot):RPS16
Chain IDs:FA (auth: Q1), OB (auth: Q2), XC (auth: Q3), GE (auth: Q4), PF (auth: Q5), YG (auth: Q6)
Chain Length:146
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S17
Gene (Uniprot):RPS17
Chain IDs:GA (auth: R1), PB (auth: R2), YC (auth: R3), HE (auth: R4), QF (auth: R5), ZG (auth: R6)
Chain Length:135
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S18
Gene (Uniprot):RPS18
Chain IDs:HA (auth: S1), QB (auth: S2), ZC (auth: S3), IE (auth: S4), RF (auth: S5), AH (auth: S6)
Chain Length:152
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S19
Gene (Uniprot):RPS19
Chain IDs:A (auth: T1), JA (auth: T2), SB (auth: T3), BD (auth: T4), KE (auth: T5), TF (auth: T6)
Chain Length:145
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S20
Gene (Uniprot):RPS20
Chain IDs:B (auth: U1), KA (auth: U2), TB (auth: U3), CD (auth: U4), LE (auth: U5), UF (auth: U6)
Chain Length:119
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S21
Gene (Uniprot):RPS21
Chain IDs:C (auth: V1), LA (auth: V2), UB (auth: V3), DD (auth: V4), ME (auth: V5), VF (auth: V6)
Chain Length:83
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15a
Gene (Uniprot):RPS15A
Chain IDs:P (auth: W1), YA (auth: W2), HC (auth: W3), QD (auth: W4), ZE (auth: W5), IG (auth: W6)
Chain Length:130
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S23
Gene (Uniprot):RPS23
Chain IDs:D (auth: X1), MA (auth: X2), VB (auth: X3), ED (auth: X4), NE (auth: X5), WF (auth: X6)
Chain Length:143
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24
Gene (Uniprot):RPS24
Chain IDs:Q (auth: Y1), ZA (auth: Y2), IC (auth: Y3), RD (auth: Y4), AF (auth: Y5), JG (auth: Y6)
Chain Length:133
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S25
Gene (Uniprot):RPS25
Chain IDs:R (auth: Z1), AB (auth: Z2), JC (auth: Z3), SD (auth: Z4), BF (auth: Z5), KG (auth: Z6)
Chain Length:125
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S26
Gene (Uniprot):RPS26
Chain IDs:E (auth: a1), NA (auth: a2), WB (auth: a3), FD (auth: a4), OE (auth: a5), XF (auth: a6)
Chain Length:115
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27
Gene (Uniprot):RPS27
Chain IDs:S (auth: b1), BB (auth: b2), KC (auth: b3), TD (auth: b4), CF (auth: b5), LG (auth: b6)
Chain Length:264
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S28
Gene (Uniprot):RPS28
Chain IDs:F (auth: c1), OA (auth: c2), XB (auth: c3), GD (auth: c4), PE (auth: c5), YF (auth: c6)
Chain Length:293
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S29
Gene (Uniprot):RPS29
Chain IDs:G (auth: d1), PA (auth: d2), YB (auth: d3), HD (auth: d4), QE (auth: d5), ZF (auth: d6)
Chain Length:56
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S30
Gene (Uniprot):FAU
Chain IDs:T (auth: e1), CB (auth: e2), LC (auth: e3), UD (auth: e4), DF (auth: e5), MG (auth: e6)
Chain Length:263
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S27a
Gene (Uniprot):RPS27A
Chain IDs:H (auth: f1), QA (auth: f2), ZB (auth: f3), ID (auth: f4), RE (auth: f5), AG (auth: f6)
Chain Length:204
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Receptor of activated protein C kinase 1
Gene (Uniprot):RACK1
Chain IDs:I (auth: g1), RA (auth: g2), AC (auth: g3), JD (auth: g4), SE (auth: g5), BG (auth: g6)
Chain Length:317
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:Human 18S ribosomal RNA
Chain IDs:U (auth: i1), DB (auth: i2), MC (auth: i3), VD (auth: i4), EF (auth: i5), NG (auth: i6)
Chain Length:1869
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L41
Gene (Uniprot):RPL41
Chain IDs:IA (auth: j1), RB (auth: j2), AD (auth: j3), JE (auth: j4), SF (auth: j5), BH (auth: j6)
Chain Length:194
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Malignant T-cell-amplified sequence 1
Gene (Uniprot):MCTS1
Chain IDs:CH (auth: k1), DH (auth: k2), EH (auth: k3), FH (auth: k4), GH (auth: k5), HH (auth: k6)
Chain Length:181
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Density-regulated protein
Gene (Uniprot):DENR
Chain IDs:IH (auth: l1), JH (auth: l2), KH (auth: l3), LH (auth: l4), MH (auth: l5), NH (auth: l6)
Chain Length:198
Number of Molecules:6
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Crystal Structure of the Human Ribosome in Complex with DENR-MCT-1.
Cell Rep 20 521 528 (2017)
PMID: 28723557 DOI: 10.1016/j.celrep.2017.06.025

Abstact

The repertoire of the density-regulated protein (DENR) and the malignant T cell-amplified sequence 1 (MCT-1/MCTS1) oncoprotein was recently expanded to include translational control of a specific set of cancer-related mRNAs. DENR and MCT-1 form the heterodimer, which binds to the ribosome and operates at both translation initiation and reinitiation steps, though by a mechanism that is yet unclear. Here, we determined the crystal structure of the human small ribosomal subunit in complex with DENR-MCT-1. The structure reveals the location of the DENR-MCT-1 dimer bound to the small ribosomal subunit. The binding site of the C-terminal domain of DENR on the ribosome has a striking similarity with those of canonical initiation factor 1 (eIF1), which controls the fidelity of translation initiation and scanning. Our findings elucidate how the DENR-MCT-1 dimer interacts with the ribosome and have functional implications for the mechanism of unconventional translation initiation and reinitiation.

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Primary Citation of related structures