5VYC

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.0 Å
  • R-Value Free: 0.321
  • R-Value Work: 0.323

Literature

Macromolecules
Sequence Display for 5VYC

Classification: RIBOSOME

Total Structure Weight: 7655375.00


Macromolecule Entities
Molecule Chains Length Organism Details
40S ribosomal protein S19 T1, T2, T3..., T4, T5, T6T1, T2, T3, T4, T5, T6 145 Homo sapiens Gene Name(s): RPS19 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S20 U1, U2, U3..., U4, U5, U6U1, U2, U3, U4, U5, U6 119 Homo sapiens Gene Name(s): RPS20 Gene View
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40S ribosomal protein S21 V1, V2, V3..., V4, V5, V6V1, V2, V3, V4, V5, V6 83 Homo sapiens Gene Name(s): RPS21 Gene View
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40S ribosomal protein S23 X1, X2, X3..., X4, X5, X6X1, X2, X3, X4, X5, X6 143 Homo sapiens Gene Name(s): RPS23 Gene View
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40S ribosomal protein S26 a1, a2, a3..., a4, a5, a6a1, a2, a3, a4, a5, a6 115 Homo sapiens Gene Name(s): RPS26 Gene View
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40S ribosomal protein S28 c1, c2, c3..., c4, c5, c6c1, c2, c3, c4, c5, c6 69 Homo sapiens Gene Name(s): RPS28 Gene View
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40S ribosomal protein S29 d1, d2, d3..., d4, d5, d6d1, d2, d3, d4, d5, d6 56 Homo sapiens Gene Name(s): RPS29 Gene View
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Ribosomal protein S27a f1, f2, f3..., f4, f5, f6f1, f2, f3, f4, f5, f6 156 Homo sapiens Gene Name(s): RPS27A Gene View
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Receptor of activated protein C kinase 1 g1, g2, g3..., g4, g5, g6g1, g2, g3, g4, g5, g6 317 Homo sapiens Gene Name(s): GNB2L1 HLC7 PIG21
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40S ribosomal protein S2 C1, C2, C3..., C4, C5, C6C1, C2, C3, C4, C5, C6 293 Homo sapiens Gene Name(s): RPS2 Gene View RPS4
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40S ribosomal protein S6 G1, G2, G3..., G4, G5, G6G1, G2, G3, G4, G5, G6 249 Homo sapiens Gene Name(s): RPS6 Gene View OK/SW-cl.2
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40S ribosomal protein S9 J1, J2, J3..., J4, J5, J6J1, J2, J3, J4, J5, J6 194 Homo sapiens Gene Name(s): RPS9 Gene View
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40S ribosomal protein S12 M1, M2, M3..., M4, M5, M6M1, M2, M3, M4, M5, M6 132 Homo sapiens Gene Name(s): RPS12 Gene View
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40S ribosomal protein S13 N1, N2, N3..., N4, N5, N6N1, N2, N3, N4, N5, N6 151 Homo sapiens Gene Name(s): RPS13 Gene View
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40S ribosomal protein S14 O1, O2, O3..., O4, O5, O6O1, O2, O3, O4, O5, O6 151 Homo sapiens Gene Name(s): RPS14 Gene View PRO2640
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40S ribosomal protein S15a W1, W2, W3..., W4, W5, W6W1, W2, W3, W4, W5, W6 130 Homo sapiens Gene Name(s): RPS15A Gene View OK/SW-cl.82
Metabolic Pathways
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40S ribosomal protein S24 Y1, Y2, Y3..., Y4, Y5, Y6Y1, Y2, Y3, Y4, Y5, Y6 133 Homo sapiens Gene Name(s): RPS24 Gene View
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40S ribosomal protein S25 Z1, Z2, Z3..., Z4, Z5, Z6Z1, Z2, Z3, Z4, Z5, Z6 125 Homo sapiens Gene Name(s): RPS25 Gene View
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40S ribosomal protein S27 b1, b2, b3..., b4, b5, b6b1, b2, b3, b4, b5, b6 84 Homo sapiens Gene Name(s): RPS27 Gene View MPS1
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40S ribosomal protein S30 e1, e2, e3..., e4, e5, e6e1, e2, e3, e4, e5, e6 133 Homo sapiens Gene Name(s):
Metabolic Pathways
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40S ribosomal protein SA A1, A2, A3..., A4, A5, A6A1, A2, A3, A4, A5, A6 295 Homo sapiens Gene Name(s): RPSA Gene View LAMBR LAMR1
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40S ribosomal protein S3a B1, B2, B3..., B4, B5, B6B1, B2, B3, B4, B5, B6 264 Homo sapiens Gene Name(s): RPS3A Gene View FTE1 MFTL
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40S ribosomal protein S3 D1, D2, D3..., D4, D5, D6D1, D2, D3, D4, D5, D6 243 Homo sapiens EC#: 4.2.99.18 IUBMB
Gene Name(s): RPS3 Gene View OK/SW-cl.26
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40S ribosomal protein S4, X isoform E1, E2, E3..., E4, E5, E6E1, E2, E3, E4, E5, E6 263 Homo sapiens Gene Name(s): RPS4X Gene View CCG2 RPS4 SCAR
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40S ribosomal protein S5 F1, F2, F3..., F4, F5, F6F1, F2, F3, F4, F5, F6 204 Homo sapiens Gene Name(s): RPS5 Gene View
Metabolic Pathways
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40S ribosomal protein S7 H1, H2, H3..., H4, H5, H6H1, H2, H3, H4, H5, H6 194 Homo sapiens Gene Name(s): RPS7 Gene View
Metabolic Pathways
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40S ribosomal protein S8 I1, I2, I3..., I4, I5, I6I1, I2, I3, I4, I5, I6 208 Homo sapiens Gene Name(s): RPS8 Gene View OK/SW-cl.83
Metabolic Pathways
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40S ribosomal protein S10 K1, K2, K3..., K4, K5, K6K1, K2, K3, K4, K5, K6 165 Homo sapiens Gene Name(s): RPS10 Gene View
Metabolic Pathways
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40S ribosomal protein S11 L1, L2, L3..., L4, L5, L6L1, L2, L3, L4, L5, L6 158 Homo sapiens Gene Name(s): RPS11 Gene View
Metabolic Pathways
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40S ribosomal protein S15 P1, P2, P3..., P4, P5, P6P1, P2, P3, P4, P5, P6 145 Homo sapiens Gene Name(s): RPS15 Gene View RIG
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40S ribosomal protein S16 Q1, Q2, Q3..., Q4, Q5, Q6Q1, Q2, Q3, Q4, Q5, Q6 146 Homo sapiens Gene Name(s): RPS16 Gene View
Metabolic Pathways
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40S ribosomal protein S17 R1, R2, R3..., R4, R5, R6R1, R2, R3, R4, R5, R6 135 Homo sapiens Gene Name(s): RPS17 Gene View RPS17L
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40S ribosomal protein S18 S1, S2, S3..., S4, S5, S6S1, S2, S3, S4, S5, S6 152 Homo sapiens Gene Name(s): RPS18 Gene View D6S218E
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60S ribosomal protein L41 j1, j2, j3..., j4, j5, j6j1, j2, j3, j4, j5, j6 25 Homo sapiens Gene Name(s): RPL41 Gene View
Metabolic Pathways
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Malignant T-cell-amplified sequence 1 k1, k2, k3..., k4, k5, k6k1, k2, k3, k4, k5, k6 181 Homo sapiens Gene Name(s): MCTS1 Gene View MCT1
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Density-regulated protein l1, l2, l3..., l4, l5, l6l1, l2, l3, l4, l5, l6 198 Homo sapiens Gene Name(s): DENR Gene View DRP1 H14
Metabolic Pathways
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Macromolecule Entities
Molecule Chains Length Organism Details
Human 18S ribosomal RNA i1, i2, i3... , i4, i5, i6 i1, i2, i3, i4, i5, i6 1869 Homo sapiens

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ZN
Query on ZN

f1, f2, f3, f4, f5, f6 ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.0 Å
  • R-Value Free: 0.321
  • R-Value Work: 0.323
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 334.67 α = 90.00
b = 597.13 β = 120.29
c = 336.50 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2017-05-24
  • Released Date: 2017-07-19
  • Deposition author(s): Lomakin, I.B., Stolboushkina, E.A., Vaidya, A.T., Garber, M.B., Dmitriev, S.E., Steitz, T.A.

Revision History

  • Version 1_0: 2017-07-19

    Type: Initial release

  • Version 1_1: 2017-08-02

    Type: Author supporting evidence, Database references