5VYC

Crystal structure of the human 40S ribosomal subunit in complex with DENR-MCT-1.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.00 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.323 
  • R-Value Observed: 0.323 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of the Human Ribosome in Complex with DENR-MCT-1.

Lomakin, I.B.Stolboushkina, E.A.Vaidya, A.T.Zhao, C.Garber, M.B.Dmitriev, S.E.Steitz, T.A.

(2017) Cell Rep 20: 521-528

  • DOI: 10.1016/j.celrep.2017.06.025
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • 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 h ...

    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.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8114, USA. Electronic address: thomas.steitz@yale.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S19
T1, T2, T3, T4, T5, T6
145Homo sapiensMutation(s): 0 
Gene Names: RPS19
Find proteins for P39019 (Homo sapiens)
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PHAROS  P39019
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S2
C1, C2, C3, C4, C5, C6
293Homo sapiensMutation(s): 0 
Gene Names: RPS2RPS4
Find proteins for P15880 (Homo sapiens)
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PHAROS  P15880
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S6
G1, G2, G3, G4, G5, G6
249Homo sapiensMutation(s): 0 
Gene Names: RPS6OK/SW-cl.2
Find proteins for P62753 (Homo sapiens)
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PHAROS  P62753
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S9
J1, J2, J3, J4, J5, J6
194Homo sapiensMutation(s): 0 
Gene Names: RPS9
Find proteins for P46781 (Homo sapiens)
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PHAROS  P46781
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S12
M1, M2, M3, M4, M5, M6
132Homo sapiensMutation(s): 0 
Gene Names: RPS12
Find proteins for P25398 (Homo sapiens)
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PHAROS  P25398
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13
N1, N2, N3, N4, N5, N6
151Homo sapiensMutation(s): 0 
Gene Names: RPS13
Find proteins for P62277 (Homo sapiens)
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PHAROS  P62277
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14
O1, O2, O3, O4, O5, O6
151Homo sapiensMutation(s): 0 
Gene Names: RPS14PRO2640
Find proteins for P62263 (Homo sapiens)
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PHAROS  P62263
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15a
W1, W2, W3, W4, W5, W6
130Homo sapiensMutation(s): 0 
Gene Names: RPS15AOK/SW-cl.82
Find proteins for P62244 (Homo sapiens)
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PHAROS  P62244
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S24
Y1, Y2, Y3, Y4, Y5, Y6
133Homo sapiensMutation(s): 0 
Gene Names: RPS24
Find proteins for P62847 (Homo sapiens)
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S25
Z1, Z2, Z3, Z4, Z5, Z6
125Homo sapiensMutation(s): 0 
Gene Names: RPS25
Find proteins for P62851 (Homo sapiens)
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27
b1, b2, b3, b4, b5, b6
84Homo sapiensMutation(s): 0 
Gene Names: RPS27MPS1
Find proteins for P42677 (Homo sapiens)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S20
U1, U2, U3, U4, U5, U6
119Homo sapiensMutation(s): 0 
Gene Names: RPS20
Find proteins for P60866 (Homo sapiens)
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PHAROS  P60866
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S30
e1, e2, e3, e4, e5, e6
133Homo sapiensMutation(s): 0 
Gene Names: FAU
Find proteins for E9PR30 (Homo sapiens)
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein SA
A1, A2, A3, A4, A5, A6
295Homo sapiensMutation(s): 0 
Gene Names: RPSALAMBRLAMR1
Find proteins for P08865 (Homo sapiens)
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PHAROS  P08865
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3a
B1, B2, B3, B4, B5, B6
264Homo sapiensMutation(s): 0 
Gene Names: RPS3AFTE1MFTL
Find proteins for P61247 (Homo sapiens)
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PHAROS  P61247
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3
D1, D2, D3, D4, D5, D6
243Homo sapiensMutation(s): 0 
Gene Names: RPS3OK/SW-cl.26
EC: 4.2.99.18
Find proteins for P23396 (Homo sapiens)
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PHAROS  P23396
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4, X isoform
E1, E2, E3, E4, E5, E6
263Homo sapiensMutation(s): 0 
Gene Names: RPS4XCCG2RPS4SCAR
Find proteins for P62701 (Homo sapiens)
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PHAROS  P62701
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S5
F1, F2, F3, F4, F5, F6
204Homo sapiensMutation(s): 0 
Gene Names: RPS5
Find proteins for P46782 (Homo sapiens)
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S7
H1, H2, H3, H4, H5, H6
194Homo sapiensMutation(s): 0 
Gene Names: RPS7
Find proteins for P62081 (Homo sapiens)
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S8
I1, I2, I3, I4, I5, I6
208Homo sapiensMutation(s): 0 
Gene Names: RPS8OK/SW-cl.83
Find proteins for P62241 (Homo sapiens)
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PHAROS  P62241
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S10
K1, K2, K3, K4, K5, K6
165Homo sapiensMutation(s): 0 
Gene Names: RPS10
Find proteins for P46783 (Homo sapiens)
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PHAROS  P46783
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S21
V1, V2, V3, V4, V5, V6
83Homo sapiensMutation(s): 0 
Gene Names: RPS21
Find proteins for P63220 (Homo sapiens)
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PHAROS  P63220
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S11
L1, L2, L3, L4, L5, L6
158Homo sapiensMutation(s): 0 
Gene Names: RPS11
Find proteins for P62280 (Homo sapiens)
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15
P1, P2, P3, P4, P5, P6
145Homo sapiensMutation(s): 0 
Gene Names: RPS15RIG
Find proteins for P62841 (Homo sapiens)
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PHAROS  P62841
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16
Q1, Q2, Q3, Q4, Q5, Q6
146Homo sapiensMutation(s): 0 
Gene Names: RPS16
Find proteins for P62249 (Homo sapiens)
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PHAROS  P62249
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S17
R1, R2, R3, R4, R5, R6
135Homo sapiensMutation(s): 0 
Gene Names: RPS17RPS17L
Find proteins for P08708 (Homo sapiens)
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PHAROS  P08708
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S18
S1, S2, S3, S4, S5, S6
152Homo sapiensMutation(s): 0 
Gene Names: RPS18D6S218E
Find proteins for P62269 (Homo sapiens)
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PHAROS  P62269
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L41
j1, j2, j3, j4, j5, j6
25Homo sapiensMutation(s): 0 
Gene Names: RPL41
Find proteins for P62945 (Homo sapiens)
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Malignant T-cell-amplified sequence 1
k1, k2, k3, k4, k5, k6
181Homo sapiensMutation(s): 0 
Gene Names: MCTS1MCT1
Find proteins for Q9ULC4 (Homo sapiens)
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PHAROS  Q9ULC4
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Density-regulated protein
l1, l2, l3, l4, l5, l6
198Homo sapiensMutation(s): 0 
Gene Names: DENRDRP1H14
Find proteins for O43583 (Homo sapiens)
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PHAROS  O43583
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23
X1, X2, X3, X4, X5, X6
143Homo sapiensMutation(s): 0 
Gene Names: RPS23
Find proteins for P62266 (Homo sapiens)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S26
a1, a2, a3, a4, a5, a6
115Homo sapiensMutation(s): 0 
Gene Names: RPS26
Find proteins for P62854 (Homo sapiens)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S28
c1, c2, c3, c4, c5, c6
69Homo sapiensMutation(s): 0 
Gene Names: RPS28
Find proteins for P62857 (Homo sapiens)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S29
d1, d2, d3, d4, d5, d6
56Homo sapiensMutation(s): 0 
Gene Names: RPS29
Find proteins for P62273 (Homo sapiens)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S27a
f1, f2, f3, f4, f5, f6
156Homo sapiensMutation(s): 0 
Gene Names: RPS27A
Find proteins for Q5RKT7 (Homo sapiens)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Receptor of activated protein C kinase 1
g1, g2, g3, g4, g5, g6
317Homo sapiensMutation(s): 0 
Gene Names: RACK1GNB2L1HLC7PIG21
Find proteins for P63244 (Homo sapiens)
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Entity ID: 21
MoleculeChainsLengthOrganism
Human 18S ribosomal RNAi1, i2,i3,i4,i5,i61869Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
f1, f2, f3, f4, f5, f6
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.00 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.323 
  • R-Value Observed: 0.323 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 334.67α = 90
b = 597.13β = 120.29
c = 336.5γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesP30KD034989
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM022778
Russian Science FoundationRussian Federation14-50-00060

Revision History 

  • Version 1.0: 2017-07-19
    Type: Initial release
  • Version 1.1: 2017-08-02
    Changes: Author supporting evidence, Database references
  • Version 1.2: 2019-12-25
    Changes: Advisory, Author supporting evidence