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The crystal structure of the eukaryotic 40S ribosomal subunit in complex with EIF1 and EIF1A

Analyse The crystal structure of the eukaryotic 40S ribosomal subunit in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
4BTS
Type
protein + RNA
Length
27,676 residues
Chains
144
Method
x-ray diffraction
Collection
MolNFT v2 / PDB Bank
Contract
0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner
0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution
3.703
Source
TETRAHYMENA THERMOPHILA; Tetrahymena thermophila SB210
Molecule
Translation initiation factor eif-1A family protein; 40S ribosomal protein RPS28E; 40S…
UniProt
I7MK25, E6PBU6, E6PBS6, E6PBS5, E6PBR8, E6PBU4, E6PBU5, E6PBS8, E6PBU3, E6PBU9, E6PBR9, E6PBS1, E6PBS7, E6PBS0, E6PBV1, E6PBS3, E6PBU0, E6PBT4, E6PBT8, E6PBT2, P06147, E6PBT6, E6PBU7, E6PBT1, E6PBU2, E6PBS9, E6PBV0, E6PBT3, E6PBT7, E6PBT0, E6PBT5, E6PBS2, E6PBU8, E6PBS4, E6PBT9
Ligands
MG, ZN
Pockets
20 · best druggability 0.90

Structure

x-ray diffraction · resolution 3.703 · 37 distinct chains · 30% helix, 24% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A0, B0, C0, D0Translation initiation factor eif-1A family proteinprotein9915% helix, 33% strandI7MK25
A1, B1, C1, D140S ribosomal protein RPS28Eprotein660% helix, 48% strandE6PBU6
A2, B2, C2, D240S ribosomal protein S8protein20726% helix, 27% strandE6PBS6
A3, B3, C3, D340S ribosomal protein RPS7Eprotein19638% helix, 24% strandE6PBS5
A440S ribosomal protein S3Aprotein20925% helix, 33% strandE6PBR8
A5, B5, C5, D540S ribosomal protein RPS26Eprotein10019% helix, 23% strandE6PBU4
A6, B6, C6, D640S ribosomal protein S27protein808% helix, 31% strandE6PBU5
A7, B7, C7, D740S ribosomal protein RPS10Eprotein10143% helix, 20% strandE6PBS8
A8, B8, C8, D840S ribosomal protein RPS25Eprotein7938% helix, 22% strandE6PBU3
A9, B9, C9, D940S ribosomal protein RPS31Eprotein9326% helix, 17% strandE6PBU9
AA, BA, CA, DA18S ribosomal RNArna1717——
AB, BB, CB, DB40S ribosomal protein saprotein20141% helix, 14% strandE6PBR9
AC, BC, CC, DC40S ribosomal protein RPS3Eprotein22834% helix, 26% strandE6PBS1
AD, BD, CD, DD40S ribosomal protein RPS9Eprotein18049% helix, 3% strandE6PBS7
AE, BE, CE, DE40S ribosomal protein RPS2Eprotein22930% helix, 27% strandE6PBS0
AF, BF, CF, DFEIF1protein8925% helix, 34% strandE6PBV1
AG, BG, CG, DG40S ribosomal protein RPS5Eprotein19252% helix, 9% strandE6PBS3
AH, BH, CH, DH40S ribosomal protein RPS22Eprotein12934% helix, 29% strandE6PBU0
AI, BI, CI, DI40S ribosomal protein RPS16Eprotein14340% helix, 20% strandE6PBT4
AJ, BJ, CJ, DJ40S ribosomal protein RPS20Eprotein10821% helix, 46% strandE6PBT8
AK, BK, CK, DK40S ribosomal protein RPS14Eprotein14026% helix, 26% strandE6PBT2
AL, BL, CL, DL40S ribosomal protein S12protein14024% helix, 29% strandP06147
AM, BM, CM, DM40S ribosomal protein RPS18Eprotein15338% helix, 6% strandE6PBT6
AN, BN, CN, DN40S ribosomal protein RPS29Eprotein5420% helix, 9% strandE6PBU7
AO, BO, CO, DO40S ribosomal protein RPS13Eprotein15254% helix, 0% strandE6PBT1
AP, BP, CP, DP40S ribosomal protein S24protein14841% helix, 24% strandE6PBU2
AQ, BQ, CQ, DQ40S ribosomal protein RPS11Eprotein1565% helix, 31% strandE6PBS9
AR, BR, CR, DR40S ribosomal protein RACK1protein3381% helix, 50% strandE6PBV0
AS, BS, CS, DS40S ribosomal protein RPS15Eprotein12834% helix, 13% strandE6PBT3
AT, BT, CT, DT40S ribosomal protein RPS19Eprotein15449% helix, 10% strandE6PBT7
AU, BU, CU, DU40S ribosomal protein RPS12Eprotein12444% helix, 17% strandE6PBT0
AV, BV, CV, DV40S ribosomal protein RPS17Eprotein11958% helix, 7% strandE6PBT5
AW, BW, CW, DW40S ribosomal protein RPS4Eprotein25916% helix, 32% strandE6PBS2
AX, BX, CX, DX40S ribosomal protein RPS30Eprotein7439% helix, 0% strandE6PBU8
AY, BY, CY, DY40S ribosomal protein S6protein22828% helix, 24% strandE6PBS4
AZ, BZ, CZ, DZ40S ribosomal protein RPS21Eprotein9725% helix, 24% strandE6PBT9
B4, C4, D440S ribosomal protein S3Aprotein22127% helix, 32% strandE6PBR8

Ligands and binding sites

  • MG · Magnesium ion · metal · 316 copies · chains AA, A5, AE, AL, AW, AP, A4, A2, AK, AT, BA, B5, BE, BL, BW, BP, B2, BK, BT, CA, C5, CE, CL, CW, CP, C4, C2, CK, CT, DA, D5, DE, DL, DW, DP, D4, D2, DK, DT
  • ZN · Zinc ion · metal · 16 copies · chains A5, A6, A9, AN, B5, B6, B9, BN, C5, C6, C9, CN, D5, D6, D9, DN

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
113980.900.93145MG
210160.900.9398MG
39160.900.9395MG
411800.890.92113MG
512290.890.91113MG

Interfaces

410 interfaces between chains.

  • AA–AY · 5110 Ų buried · 123 hydrogen bonds · protein-nucleic
  • DA–DY · 5090 Ų buried · 125 hydrogen bonds · protein-nucleic
  • CA–CY · 5074 Ų buried · 123 hydrogen bonds · protein-nucleic
  • BA–BY · 5042 Ų buried · 124 hydrogen bonds · protein-nucleic
  • C2–CA · 4482 Ų buried · 123 hydrogen bonds · protein-nucleic

Compared structures

  • P06147 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S12 (P06147) · a predicted model of the same protein · chain AL against A, TM-score 0.97

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