4V9J

70S ribosome translocation intermediate GDPNP-II containing elongation factor EFG/GDPNP, mRNA, and tRNA bound in the pe*/E state.

This is a large structure.

> Summary

Summary for 4V9J

Integrates4KBT 4KBU 4KBV 4KBW
Related PRD IDPRD_000226
DescriptorRibosome
Functional Keywordsgdpnp, chimeric hybrid state ribosome, translocation intermediate, ef-g, mrna, trna, ribosome-antibiotic complex, ribosome/antibiotic
Biological sourceThermus thermophilus
More
Cellular locationCytoplasm  Q72I01
Total number of polymer chains122
Total molecular weight4566590.96
Authors
Zhou, J.,Lancaster, L.,Donohue, J.P.,Noller, H.F. (deposition date: 2013-04-23, release date: 2014-07-09, modification date: 2014-12-10)
Primary citation
Zhou, J.,Lancaster, L.,Donohue, J.P.,Noller, H.F.
Crystal structures of EF-G-ribosome complexes trapped in intermediate states of translocation.
Science, 340:1236086-1236086, 2013
PubMed: 23812722
DOI: 10.1126/science.1236086
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (3.86 Å)

More Asymmetric unit images

Molmil generated image of 4v9j
no rotation
Molmil generated image of 4v9j
rotated about x axis by 90°
Molmil generated image of 4v9j
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
AB, CB30S ribosomal protein S2polymer23527116.42
UniProt (P62662)
Pfam (PF00318)
Thermus thermophilus
AC, CC30S ribosomal protein S3polymer20722975.62
UniProt (P62663)
Pfam (PF00189)
Pfam (PF07650)
Thermus thermophilus
AD, CD30S ribosomal protein S4polymer20824242.32
UniProt (P62664)
Pfam (PF00163)
Pfam (PF01479)
Thermus thermophilus
AE, CE30S ribosomal protein S5polymer15116460.22
UniProt (P62665)
Pfam (PF00333)
Pfam (PF03719)
Thermus thermophilus
AF, CF30S ribosomal protein S6polymer10111988.82
UniProt (P62666)
Pfam (PF01250)
Thermus thermophilusTS9
AG, CG30S ribosomal protein S7polymer15517919.82
UniProt (P62667)
Pfam (PF00177)
Thermus thermophilus
AH, CH30S ribosomal protein S8polymer13815868.62
UniProt (P62668)
Pfam (PF00410)
Thermus thermophilus
AI, CI30S ribosomal protein S9polymer12714298.52
UniProt (P62669)
Pfam (PF00380)
Thermus thermophilus
AJ, CJ30S ribosomal protein S10polymer9911398.32
UniProt (P62653)
Pfam (PF00338)
Thermus thermophilus
AK, CK30S ribosomal protein S11polymer11912606.42
UniProt (P62654)
Pfam (PF00411)
Thermus thermophilus
AL, CL30S ribosomal protein S12polymer12513875.42
UniProt (P61941)
Pfam (PF00164)
Thermus thermophilus
AM, CM30S ribosomal protein S13polymer12514207.72
UniProt (P62655)
Pfam (PF00416)
Thermus thermophilus
AN, CN30S ribosomal protein S14 type Zpolymer607027.52
UniProt (P62656)
Pfam (PF00253)
Thermus thermophilus
AO, CO30S ribosomal protein S15polymer8810447.22
UniProt (P62657)
Pfam (PF00312)
Thermus thermophilus
AP, CP30S ribosomal protein S16polymer849995.52
UniProt (P62238)
Pfam (PF00886)
Thermus thermophilus
AQ, CQ30S ribosomal protein S17polymer10011879.12
UniProt (P62658)
Pfam (PF00366)
Thermus thermophilus
AR, CR30S ribosomal protein S18polymer708155.82
UniProt (P62659)
Pfam (PF01084)
Thermus thermophilus
AS, CS30S ribosomal protein S19polymer799006.52
UniProt (P62660)
Pfam (PF00203)
Thermus thermophilus
AT, CT30S ribosomal protein S20polymer9910907.12
UniProt (P62661)
Pfam (PF01649)
Thermus thermophilus
AA, CA16S ribosomal RNApolymer1511490593.52
Thermus thermophilus
AV, CVmessenger RNApolymer185907.62
Thermus thermophilus
AW, CWtRNA-Metpolymer7724728.72
Escherichia coli
AY, CYElongation factor Gpolymer68776547.62
UniProt (Q72I01)
Pfam (PF00009)
Pfam (PF00679)
Pfam (PF03144)
Pfam (PF03764)
Pfam (PF14492)
Thermus thermophilusEF-G
AU, CUViomycinpolymer6703.72
NOR (NOR00633)
Streptomyces
BC, DC50S ribosomal protein L1polymer22824741.52
UniProt (Q72GV9)
Pfam (PF00687)
Thermus thermophilus
BD, DD50S ribosomal protein L2polymer27530401.42
UniProt (Q72I07)
Pfam (PF00181)
Pfam (PF03947)
Thermus thermophilus
BE, DE50S ribosomal protein L3polymer20522321.02
UniProt (Q72I04)
Pfam (PF00297)
Thermus thermophilus
BF, DF50S ribosomal protein L4polymer20823071.72
UniProt (Q72I05)
Pfam (PF00573)
Thermus thermophilusL1e
BG, DG50S ribosomal protein L5polymer18120930.42
UniProt (Q72I16)
Pfam (PF00281)
Pfam (PF00673)
Thermus thermophilus
BH, DH50S ribosomal protein L6polymer16718088.02
UniProt (Q72I19)
Pfam (PF00347)
Thermus thermophilus
BJ, DJ50S ribosomal protein L10polymer17014485.82
Thermus thermophilus
BK, DK50S ribosomal protein L11polymer14014754.22
UniProt (P62442)
Pfam (PF00298)
Pfam (PF03946)
Thermus thermophilus
BO, DO50S ribosomal protein L14polymer12213323.62
UniProt (Q72I14)
Pfam (PF00238)
Thermus thermophilus
BP, DP50S ribosomal protein L15polymer14615858.52
UniProt (Q72I23)
Pfam (PF00828)
Thermus thermophilus
BQ, DQ50S ribosomal protein L16polymer14115993.92
UniProt (Q72I11)
Pfam (PF00252)
Thermus thermophilus
BR, DR50S ribosomal protein L17polymer11713619.02
UniProt (Q72I33)
Pfam (PF01196)
Thermus thermophilus
BS, DS50S ribosomal protein L18polymer9910998.92
UniProt (Q72I20)
Pfam (PF00861)
Thermus thermophilusTL24
BT, DT50S ribosomal protein L19polymer13816289.92
UniProt (Q72JU9)
Pfam (PF01245)
Thermus thermophilus
BU, DU50S ribosomal protein L20polymer11713648.12
UniProt (Q72L76)
Pfam (PF00453)
Thermus thermophilus
BV, DV50S ribosomal protein L21polymer10111069.22
UniProt (Q72HR2)
Pfam (PF00829)
Thermus thermophilus
BW, DW50S ribosomal protein L22polymer11312808.12
UniProt (Q72I09)
Pfam (PF00237)
Thermus thermophilus
BX, DX50S ribosomal protein L23polymer9310386.32
UniProt (Q72I06)
Pfam (PF00276)
Thermus thermophilus
BY, DY50S ribosomal protein L24polymer10711696.22
UniProt (Q72I15)
Pfam (PF00467)
Pfam (PF17136)
Thermus thermophilus
BZ, DZ50S ribosomal protein L25polymer18520879.02
UniProt (Q72IA7)
Pfam (PF01386)
Pfam (PF14693)
Thermus thermophilusTL5
B0, D050S ribosomal protein L27polymer849397.92
UniProt (Q72HR3)
Pfam (PF01016)
Thermus thermophilus
B1, D150S ribosomal protein L28polymer9310430.42
UniProt (Q72G84)
Pfam (PF00830)
Thermus thermophilus
B4, D450S ribosomal protein L31polymer353893.62
UniProt (Q72JR0)
Pfam (PF01197)
Thermus thermophilus
BN, DN50S ribosomal protein L13polymer13815699.72
UniProt (Q72IN1)
Pfam (PF00572)
Thermus thermophilus
B2, D250S ribosomal protein L29polymer718539.12
UniProt (Q72I12)
Pfam (PF00831)
Thermus thermophilus
B3, D350S ribosomal protein L30polymer606799.12
UniProt (Q72I22)
Pfam (PF00327)
Thermus thermophilus
B5, D550S ribosomal protein L32polymer596590.92
UniProt (P62652)
Pfam (PF01783)
Thermus thermophilus
B6, D650S ribosomal protein L33polymer506214.42
UniProt (Q72GW3)
Pfam (PF00471)
Thermus thermophilus
B7, D750S ribosomal protein L34polymer496132.42
UniProt (P80340)
Pfam (PF00468)
Thermus thermophilus
B8, D850S ribosomal protein L35polymer647375.02
UniProt (Q72L77)
Pfam (PF01632)
Thermus thermophilus
B9, D950S ribosomal protein L36polymer374435.42
UniProt (Q72I28)
Pfam (PF00444)
Thermus thermophilusRibosomal protein B
Be, De50S ribosomal protein L7/L12polymer10310280.12
UniProt (Q72GS2)
Pfam (PF00542)
Pfam (PF16320)
Thermus thermophilus
Bf, Bg, Df, Dg50S ribosomal protein L7/L12polymer312656.34
Thermus thermophilus
Bh, Dh50S ribosomal protein L7/L12polymer302571.22
Thermus thermophilus
BB, DB5S ribosomal RNApolymer11938553.02
Thermus thermophilus
BA, DA23S ribosomal RNApolymer2879936302.12
Thermus thermophilus
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTERnon-polymer522.22
MAGNESIUM IONnon-polymer24.32

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains122
Total molecular weight4565498.0
Non-Polymers*Number of molecules4
Total molecular weight1093.0
All*Total molecular weight4566591.0
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (3.86 Å)

Cell axes302.391683.918356.698
Cell angles90.0090.0090.00
SpacegroupC 1 2 1
Resolution limits40.00 - 3.86
the highest resolution shell value -
R-factor0.264
R-work0.26400
R-free0.31660
RMSD bond length0.022
RMSD bond angle1.101

Data Collection Statistics

Resolution limits40.00 - 3.86
the highest resolution shell value -
Number of reflections462446
Completeness96.0
Redundancy3.8
I/sigma(I)1.5

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

?

Functional Information from GO Data

ChainGOidnamespacecontents
AY0005737cellular_componentcytoplasm
AY0005525molecular_functionGTP binding
AY0003924molecular_functionGTPase activity
AY0003746molecular_functiontranslation elongation factor activity
CY0005737cellular_componentcytoplasm
CY0005525molecular_functionGTP binding
CY0003924molecular_functionGTPase activity
CY0003746molecular_functiontranslation elongation factor activity
BK0005840cellular_componentribosome
BK0070180molecular_functionlarge ribosomal subunit rRNA binding
BK0003735molecular_functionstructural constituent of ribosome
BK0006412biological_processtranslation
DK0005840cellular_componentribosome
DK0070180molecular_functionlarge ribosomal subunit rRNA binding
DK0003735molecular_functionstructural constituent of ribosome
DK0006412biological_processtranslation
BN0005840cellular_componentribosome
BN0003735molecular_functionstructural constituent of ribosome
BN0006412biological_processtranslation
DN0005840cellular_componentribosome
DN0003735molecular_functionstructural constituent of ribosome
DN0006412biological_processtranslation
BO0015934cellular_componentlarge ribosomal subunit
BO0019843molecular_functionrRNA binding
BO0003735molecular_functionstructural constituent of ribosome
BO0006412biological_processtranslation
DO0015934cellular_componentlarge ribosomal subunit
DO0019843molecular_functionrRNA binding
DO0003735molecular_functionstructural constituent of ribosome
DO0006412biological_processtranslation
BP0015934cellular_componentlarge ribosomal subunit
BP0019843molecular_functionrRNA binding
BP0003735molecular_functionstructural constituent of ribosome
BP0006412biological_processtranslation
DP0015934cellular_componentlarge ribosomal subunit
DP0019843molecular_functionrRNA binding
DP0003735molecular_functionstructural constituent of ribosome
DP0006412biological_processtranslation
BQ0005840cellular_componentribosome
BQ0019843molecular_functionrRNA binding
BQ0003735molecular_functionstructural constituent of ribosome
BQ0000049molecular_functiontRNA binding
BQ0006412biological_processtranslation
DQ0005840cellular_componentribosome
DQ0019843molecular_functionrRNA binding
DQ0003735molecular_functionstructural constituent of ribosome
DQ0000049molecular_functiontRNA binding
DQ0006412biological_processtranslation
BR0005840cellular_componentribosome
BR0003735molecular_functionstructural constituent of ribosome
BR0006412biological_processtranslation
DR0005840cellular_componentribosome
DR0003735molecular_functionstructural constituent of ribosome
DR0006412biological_processtranslation
BS0005840cellular_componentribosome
BS0019843molecular_functionrRNA binding
BS0003735molecular_functionstructural constituent of ribosome
BS0006412biological_processtranslation
DS0005840cellular_componentribosome
DS0019843molecular_functionrRNA binding
DS0003735molecular_functionstructural constituent of ribosome
DS0006412biological_processtranslation
BT0005840cellular_componentribosome
BT0003735molecular_functionstructural constituent of ribosome
BT0006412biological_processtranslation
DT0005840cellular_componentribosome
DT0003735molecular_functionstructural constituent of ribosome
DT0006412biological_processtranslation
BC0015934cellular_componentlarge ribosomal subunit
BC0019843molecular_functionrRNA binding
BC0003735molecular_functionstructural constituent of ribosome
BC0000049molecular_functiontRNA binding
BC0006417biological_processregulation of translation
BC0006412biological_processtranslation
DC0015934cellular_componentlarge ribosomal subunit
DC0019843molecular_functionrRNA binding
DC0003735molecular_functionstructural constituent of ribosome
DC0000049molecular_functiontRNA binding
DC0006417biological_processregulation of translation
DC0006412biological_processtranslation
BU0005840cellular_componentribosome
BU0019843molecular_functionrRNA binding
BU0003735molecular_functionstructural constituent of ribosome
BU0000027biological_processribosomal large subunit assembly
BU0006412biological_processtranslation
DU0005840cellular_componentribosome
DU0019843molecular_functionrRNA binding
DU0003735molecular_functionstructural constituent of ribosome
DU0000027biological_processribosomal large subunit assembly
DU0006412biological_processtranslation
BV0005840cellular_componentribosome
BV0019843molecular_functionrRNA binding
BV0003735molecular_functionstructural constituent of ribosome
BV0006412biological_processtranslation
DV0005840cellular_componentribosome
DV0019843molecular_functionrRNA binding
DV0003735molecular_functionstructural constituent of ribosome
DV0006412biological_processtranslation
BW0015934cellular_componentlarge ribosomal subunit
BW0019843molecular_functionrRNA binding
BW0003735molecular_functionstructural constituent of ribosome
BW0006412biological_processtranslation
DW0015934cellular_componentlarge ribosomal subunit
DW0019843molecular_functionrRNA binding
DW0003735molecular_functionstructural constituent of ribosome
DW0006412biological_processtranslation
BX0005840cellular_componentribosome
BX0000166molecular_functionnucleotide binding
BX0019843molecular_functionrRNA binding
BX0003735molecular_functionstructural constituent of ribosome
BX0006412biological_processtranslation
DX0005840cellular_componentribosome
DX0000166molecular_functionnucleotide binding
DX0019843molecular_functionrRNA binding
DX0003735molecular_functionstructural constituent of ribosome
DX0006412biological_processtranslation
BY0005840cellular_componentribosome
BY0019843molecular_functionrRNA binding
BY0003735molecular_functionstructural constituent of ribosome
BY0006412biological_processtranslation
DY0005840cellular_componentribosome
DY0019843molecular_functionrRNA binding
DY0003735molecular_functionstructural constituent of ribosome
DY0006412biological_processtranslation
BZ0005840cellular_componentribosome
BZ0008097molecular_function5S rRNA binding
BZ0003735molecular_functionstructural constituent of ribosome
BZ0006412biological_processtranslation
DZ0005840cellular_componentribosome
DZ0008097molecular_function5S rRNA binding
DZ0003735molecular_functionstructural constituent of ribosome
DZ0006412biological_processtranslation
B00005840cellular_componentribosome
B00003735molecular_functionstructural constituent of ribosome
B00006412biological_processtranslation
D00005840cellular_componentribosome
D00003735molecular_functionstructural constituent of ribosome
D00006412biological_processtranslation
B10005840cellular_componentribosome
B10003735molecular_functionstructural constituent of ribosome
B10006412biological_processtranslation
D10005840cellular_componentribosome
D10003735molecular_functionstructural constituent of ribosome
D10006412biological_processtranslation
B20005840cellular_componentribosome
B20003735molecular_functionstructural constituent of ribosome
B20006412biological_processtranslation
D20005840cellular_componentribosome
D20003735molecular_functionstructural constituent of ribosome
D20006412biological_processtranslation
BD0015934cellular_componentlarge ribosomal subunit
BD0019843molecular_functionrRNA binding
BD0003735molecular_functionstructural constituent of ribosome
BD0016740molecular_functiontransferase activity
BD0006412biological_processtranslation
DD0015934cellular_componentlarge ribosomal subunit
DD0019843molecular_functionrRNA binding
DD0003735molecular_functionstructural constituent of ribosome
DD0016740molecular_functiontransferase activity
DD0006412biological_processtranslation
B30015934cellular_componentlarge ribosomal subunit
B30003735molecular_functionstructural constituent of ribosome
B30006412biological_processtranslation
D30015934cellular_componentlarge ribosomal subunit
D30003735molecular_functionstructural constituent of ribosome
D30006412biological_processtranslation
B40005840cellular_componentribosome
B40046872molecular_functionmetal ion binding
B40019843molecular_functionrRNA binding
B40003735molecular_functionstructural constituent of ribosome
B40006412biological_processtranslation
D40005840cellular_componentribosome
D40046872molecular_functionmetal ion binding
D40019843molecular_functionrRNA binding
D40003735molecular_functionstructural constituent of ribosome
D40006412biological_processtranslation
B50015934cellular_componentlarge ribosomal subunit
B50003735molecular_functionstructural constituent of ribosome
B50006412biological_processtranslation
D50015934cellular_componentlarge ribosomal subunit
D50003735molecular_functionstructural constituent of ribosome
D50006412biological_processtranslation
B60005840cellular_componentribosome
B60003735molecular_functionstructural constituent of ribosome
B60006412biological_processtranslation
D60005840cellular_componentribosome
D60003735molecular_functionstructural constituent of ribosome
D60006412biological_processtranslation
B70005840cellular_componentribosome
B70003735molecular_functionstructural constituent of ribosome
B70006412biological_processtranslation
D70005840cellular_componentribosome
D70003735molecular_functionstructural constituent of ribosome
D70006412biological_processtranslation
B80005840cellular_componentribosome
B80003735molecular_functionstructural constituent of ribosome
B80006412biological_processtranslation
D80005840cellular_componentribosome
D80003735molecular_functionstructural constituent of ribosome
D80006412biological_processtranslation
B90005840cellular_componentribosome
B90003735molecular_functionstructural constituent of ribosome
B90006412biological_processtranslation
D90005840cellular_componentribosome
D90003735molecular_functionstructural constituent of ribosome
D90006412biological_processtranslation
BE0005840cellular_componentribosome
BE0019843molecular_functionrRNA binding
BE0003735molecular_functionstructural constituent of ribosome
BE0006412biological_processtranslation
DE0005840cellular_componentribosome
DE0019843molecular_functionrRNA binding
DE0003735molecular_functionstructural constituent of ribosome
DE0006412biological_processtranslation
BF0005840cellular_componentribosome
BF0019843molecular_functionrRNA binding
BF0003735molecular_functionstructural constituent of ribosome
BF0006412biological_processtranslation
DF0005840cellular_componentribosome
DF0019843molecular_functionrRNA binding
DF0003735molecular_functionstructural constituent of ribosome
DF0006412biological_processtranslation
BG0005840cellular_componentribosome
BG0019843molecular_functionrRNA binding
BG0003735molecular_functionstructural constituent of ribosome
BG0000049molecular_functiontRNA binding
BG0006412biological_processtranslation
DG0005840cellular_componentribosome
DG0019843molecular_functionrRNA binding
DG0003735molecular_functionstructural constituent of ribosome
DG0000049molecular_functiontRNA binding
DG0006412biological_processtranslation
BH0005840cellular_componentribosome
BH0019843molecular_functionrRNA binding
BH0003735molecular_functionstructural constituent of ribosome
BH0006412biological_processtranslation
DH0005840cellular_componentribosome
DH0019843molecular_functionrRNA binding
DH0003735molecular_functionstructural constituent of ribosome
DH0006412biological_processtranslation
Be0005840cellular_componentribosome
Be0003735molecular_functionstructural constituent of ribosome
Be0006412biological_processtranslation
De0005840cellular_componentribosome
De0003735molecular_functionstructural constituent of ribosome
De0006412biological_processtranslation
AJ0005840cellular_componentribosome
AJ0003735molecular_functionstructural constituent of ribosome
AJ0000049molecular_functiontRNA binding
AJ0006412biological_processtranslation
CJ0005840cellular_componentribosome
CJ0003735molecular_functionstructural constituent of ribosome
CJ0000049molecular_functiontRNA binding
CJ0006412biological_processtranslation
AK0005840cellular_componentribosome
AK0019843molecular_functionrRNA binding
AK0003735molecular_functionstructural constituent of ribosome
AK0006412biological_processtranslation
CK0005840cellular_componentribosome
CK0019843molecular_functionrRNA binding
CK0003735molecular_functionstructural constituent of ribosome
CK0006412biological_processtranslation
AL0015935cellular_componentsmall ribosomal subunit
AL0019843molecular_functionrRNA binding
AL0003735molecular_functionstructural constituent of ribosome
AL0000049molecular_functiontRNA binding
AL0006412biological_processtranslation
CL0015935cellular_componentsmall ribosomal subunit
CL0019843molecular_functionrRNA binding
CL0003735molecular_functionstructural constituent of ribosome
CL0000049molecular_functiontRNA binding
CL0006412biological_processtranslation
AM0005840cellular_componentribosome
AM0019843molecular_functionrRNA binding
AM0003735molecular_functionstructural constituent of ribosome
AM0000049molecular_functiontRNA binding
AM0006412biological_processtranslation
CM0005840cellular_componentribosome
CM0019843molecular_functionrRNA binding
CM0003735molecular_functionstructural constituent of ribosome
CM0000049molecular_functiontRNA binding
CM0006412biological_processtranslation
AN0005840cellular_componentribosome
AN0019843molecular_functionrRNA binding
AN0003735molecular_functionstructural constituent of ribosome
AN0008270molecular_functionzinc ion binding
AN0006412biological_processtranslation
CN0005840cellular_componentribosome
CN0019843molecular_functionrRNA binding
CN0003735molecular_functionstructural constituent of ribosome
CN0008270molecular_functionzinc ion binding
CN0006412biological_processtranslation
AO0005840cellular_componentribosome
AO0019843molecular_functionrRNA binding
AO0003735molecular_functionstructural constituent of ribosome
AO0006412biological_processtranslation
CO0005840cellular_componentribosome
CO0019843molecular_functionrRNA binding
CO0003735molecular_functionstructural constituent of ribosome
CO0006412biological_processtranslation
AP0005840cellular_componentribosome
AP0019843molecular_functionrRNA binding
AP0003735molecular_functionstructural constituent of ribosome
AP0006412biological_processtranslation
CP0005840cellular_componentribosome
CP0019843molecular_functionrRNA binding
CP0003735molecular_functionstructural constituent of ribosome
CP0006412biological_processtranslation
AQ0005840cellular_componentribosome
AQ0019843molecular_functionrRNA binding
AQ0003735molecular_functionstructural constituent of ribosome
AQ0006412biological_processtranslation
CQ0005840cellular_componentribosome
CQ0019843molecular_functionrRNA binding
CQ0003735molecular_functionstructural constituent of ribosome
CQ0006412biological_processtranslation
AR0005840cellular_componentribosome
AR0019843molecular_functionrRNA binding
AR0003735molecular_functionstructural constituent of ribosome
AR0006412biological_processtranslation
CR0005840cellular_componentribosome
CR0019843molecular_functionrRNA binding
CR0003735molecular_functionstructural constituent of ribosome
CR0006412biological_processtranslation
AS0015935cellular_componentsmall ribosomal subunit
AS0019843molecular_functionrRNA binding
AS0003735molecular_functionstructural constituent of ribosome
AS0006412biological_processtranslation
CS0015935cellular_componentsmall ribosomal subunit
CS0019843molecular_functionrRNA binding
CS0003735molecular_functionstructural constituent of ribosome
CS0006412biological_processtranslation
AT0005840cellular_componentribosome
AT0019843molecular_functionrRNA binding
AT0003735molecular_functionstructural constituent of ribosome
AT0006412biological_processtranslation
CT0005840cellular_componentribosome
CT0019843molecular_functionrRNA binding
CT0003735molecular_functionstructural constituent of ribosome
CT0006412biological_processtranslation
AB0015935cellular_componentsmall ribosomal subunit
AB0019843molecular_functionrRNA binding
AB0003735molecular_functionstructural constituent of ribosome
AB0006412biological_processtranslation
CB0015935cellular_componentsmall ribosomal subunit
CB0019843molecular_functionrRNA binding
CB0003735molecular_functionstructural constituent of ribosome
CB0006412biological_processtranslation
AC0015935cellular_componentsmall ribosomal subunit
AC0003729molecular_functionmRNA binding
AC0019843molecular_functionrRNA binding
AC0003735molecular_functionstructural constituent of ribosome
AC0006412biological_processtranslation
CC0015935cellular_componentsmall ribosomal subunit
CC0003729molecular_functionmRNA binding
CC0019843molecular_functionrRNA binding
CC0003735molecular_functionstructural constituent of ribosome
CC0006412biological_processtranslation
AD0015935cellular_componentsmall ribosomal subunit
AD0046872molecular_functionmetal ion binding
AD0019843molecular_functionrRNA binding
AD0003735molecular_functionstructural constituent of ribosome
AD0006412biological_processtranslation
CD0015935cellular_componentsmall ribosomal subunit
CD0046872molecular_functionmetal ion binding
CD0019843molecular_functionrRNA binding
CD0003735molecular_functionstructural constituent of ribosome
CD0006412biological_processtranslation
AE0015935cellular_componentsmall ribosomal subunit
AE0019843molecular_functionrRNA binding
AE0003735molecular_functionstructural constituent of ribosome
AE0006412biological_processtranslation
CE0015935cellular_componentsmall ribosomal subunit
CE0019843molecular_functionrRNA binding
CE0003735molecular_functionstructural constituent of ribosome
CE0006412biological_processtranslation
AF0005840cellular_componentribosome
AF0019843molecular_functionrRNA binding
AF0003735molecular_functionstructural constituent of ribosome
AF0006412biological_processtranslation
CF0005840cellular_componentribosome
CF0019843molecular_functionrRNA binding
CF0003735molecular_functionstructural constituent of ribosome
CF0006412biological_processtranslation
AG0015935cellular_componentsmall ribosomal subunit
AG0019843molecular_functionrRNA binding
AG0003735molecular_functionstructural constituent of ribosome
AG0000049molecular_functiontRNA binding
AG0006412biological_processtranslation
CG0015935cellular_componentsmall ribosomal subunit
CG0019843molecular_functionrRNA binding
CG0003735molecular_functionstructural constituent of ribosome
CG0000049molecular_functiontRNA binding
CG0006412biological_processtranslation
AH0005840cellular_componentribosome
AH0019843molecular_functionrRNA binding
AH0003735molecular_functionstructural constituent of ribosome
AH0006412biological_processtranslation
CH0005840cellular_componentribosome
CH0019843molecular_functionrRNA binding
CH0003735molecular_functionstructural constituent of ribosome
CH0006412biological_processtranslation
AI0005840cellular_componentribosome
AI0019843molecular_functionrRNA binding
AI0003735molecular_functionstructural constituent of ribosome
AI0000049molecular_functiontRNA binding
AI0006412biological_processtranslation
CI0005840cellular_componentribosome
CI0019843molecular_functionrRNA binding
CI0003735molecular_functionstructural constituent of ribosome
CI0000049molecular_functiontRNA binding
CI0006412biological_processtranslation
?

Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC116binding site for residue GNP AY 701
ChainResidue
AYILE21
AYASP22
AYALA23
AYGLY24
AYLYS25
AYTHR26
AYTHR27
AYASP53
AYILE63
AYTHR64
AYTHR84
AYASN137
AYASP140
AYSER262
AYLEU264
AYMG702

AC24binding site for residue MG AY 702
ChainResidue
AYTHR26
AYTHR64
AYTHR84
AYGNP701

AC35binding site for residue MG CY 701
ChainResidue
CYLYS25
CYTHR26
CYTHR64
CYTHR84
CYGNP702

AC416binding site for residue GNP CY 702
ChainResidue
CYILE21
CYASP22
CYALA23
CYGLY24
CYLYS25
CYTHR26
CYTHR27
CYASP53
CYILE63
CYTHR64
CYTHR84
CYGLY86
CYASN137
CYLYS138
CYASP140
CYMG701

AC57binding site for Ligand residues UAL AU 5 through SER AU 3 bound to SER AU 4
ChainResidue
AAG1405
AAA1408
AAG1491
AAA1492
AAA1493
AAG1494
AUSER4

AC68binding site for Ligand residues UAL CU 5 through SER CU 3 bound to SER CU 4
ChainResidue
CAG1405
CAA1408
CAG1491
CAA1492
CAA1493
CAG1494
CUSER4
DAC1914

?

Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
5OH_4v9j_AU_66(2S)-amino[(4R,6S)-2-amino-6-hydroxy-3,4,5,6-tetrahydropyrimidin-4-yl]ethanoic acid binding site
ChainResidueligand
ALTHR445OH: (2S)-amino[(4R,6S)-2-amino-6-hydroxy-3,4,5,6-tetrahydropyrimidin-4-yl]ethanoic acid
AAG1491-A14935OH: (2S)-amino[(4R,6S)-2-amino-6-hydroxy-3,4,5,6-tetrahydropyrimidin-4-yl]ethanoic acid
AUSER3-SER45OH: (2S)-amino[(4R,6S)-2-amino-6-hydroxy-3,4,5,6-tetrahydropyrimidin-4-yl]ethanoic acid

KBE_4v9j_AU_19beta-lysine binding site
ChainResidueligand
AAC1404-U1406KBE: beta-lysine
AAA1408KBE: beta-lysine
AAG1491KBE: beta-lysine
AAA1493-U1495KBE: beta-lysine
AUSER3KBE: beta-lysine

DPP_4v9j_AU_28DIAMINOPROPANOIC ACID binding site
ChainResidueligand
AAA1408-C1409DPP: DIAMINOPROPANOIC ACID
AAG1491-G1494DPP: DIAMINOPROPANOIC ACID
AUSER3-SER4DPP: DIAMINOPROPANOIC ACID

UAL_4v9j_AU_56(2Z)-2-amino-3-(carbamoylamino)prop-2-enoic acid binding site
ChainResidueligand
AAG1491UAL: (2Z)-2-amino-3-(carbamoylamino)prop-2-enoic acid
AAA1493UAL: (2Z)-2-amino-3-(carbamoylamino)prop-2-enoic acid
AUSER3-SER4UAL: (2Z)-2-amino-3-(carbamoylamino)prop-2-enoic acid
BAA1913-C1914UAL: (2Z)-2-amino-3-(carbamoylamino)prop-2-enoic acid

GNP_4v9j_AY_70120PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER binding site
ChainResidueligand
AYILE21-THR27GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
AYASP53GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
AYILE63-THR64GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
AYTHR84GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
AYGLY86GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
AYVAL88GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
AYASN137-LYS138GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
AYASP140-LYS141GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
AYSER262-LEU264GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER

5OH_4v9j_CU_66(2S)-amino[(4R,6S)-2-amino-6-hydroxy-3,4,5,6-tetrahydropyrimidin-4-yl]ethanoic acid binding site
ChainResidueligand
CLTHR445OH: (2S)-amino[(4R,6S)-2-amino-6-hydroxy-3,4,5,6-tetrahydropyrimidin-4-yl]ethanoic acid
CAG1491-A14935OH: (2S)-amino[(4R,6S)-2-amino-6-hydroxy-3,4,5,6-tetrahydropyrimidin-4-yl]ethanoic acid
CUSER3-SER45OH: (2S)-amino[(4R,6S)-2-amino-6-hydroxy-3,4,5,6-tetrahydropyrimidin-4-yl]ethanoic acid

KBE_4v9j_CU_19beta-lysine binding site
ChainResidueligand
CAC1404-A1408KBE: beta-lysine
CAA1493-U1495KBE: beta-lysine
CUSER3KBE: beta-lysine

DPP_4v9j_CU_28DIAMINOPROPANOIC ACID binding site
ChainResidueligand
CAA1408-C1409DPP: DIAMINOPROPANOIC ACID
CAG1491-G1494DPP: DIAMINOPROPANOIC ACID
CUSER3-SER4DPP: DIAMINOPROPANOIC ACID

UAL_4v9j_CU_55(2Z)-2-amino-3-(carbamoylamino)prop-2-enoic acid binding site
ChainResidueligand
CAG1491UAL: (2Z)-2-amino-3-(carbamoylamino)prop-2-enoic acid
CUSER3-SER4UAL: (2Z)-2-amino-3-(carbamoylamino)prop-2-enoic acid
DAA1913-C1914UAL: (2Z)-2-amino-3-(carbamoylamino)prop-2-enoic acid

GNP_4v9j_CY_70222PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER binding site
ChainResidueligand
CYALA19-THR27GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
CYASP53GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
CYILE63-THR64GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
CYTHR84GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
CYGLY86GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
CYVAL88GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
CYASN137-LYS138GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
CYASP140-LYS141GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
CYSER262-LEU264GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER

?

Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
PS012082
ChainResidueDetails
BANA*
DANA*

?

Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI33GTP. {ECO:0000255|HAMAP-Rule:MF_00054}.
ChainResidueDetails
AYNA*
AYNA*
AYNA*

SWS_FT_FI53GTP. {ECO:0000255|HAMAP-Rule:MF_00054}.
ChainResidueDetails
CYNA*
CYNA*
CYNA*

?

Catalytic Information from CSA

site_idNumber of ResiduesDetails
?

Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

Sequence navigator - 4v9j: Chain AB,CB
Sequence navigator - 4v9j: Chain AC,CC
Sequence navigator - 4v9j: Chain AD,CD
Sequence navigator - 4v9j: Chain AE,CE
Sequence navigator - 4v9j: Chain AF,CF
Sequence navigator - 4v9j: Chain AG,CG
Sequence navigator - 4v9j: Chain AH,CH
Sequence navigator - 4v9j: Chain AI,CI
Sequence navigator - 4v9j: Chain AJ,CJ
Sequence navigator - 4v9j: Chain AK,CK
Sequence navigator - 4v9j: Chain AL,CL
Sequence navigator - 4v9j: Chain AM,CM
Sequence navigator - 4v9j: Chain AN,CN
Sequence navigator - 4v9j: Chain AO,CO
Sequence navigator - 4v9j: Chain AP,CP
Sequence navigator - 4v9j: Chain AQ,CQ
Sequence navigator - 4v9j: Chain AR,CR
Sequence navigator - 4v9j: Chain AS,CS
Sequence navigator - 4v9j: Chain AT,CT
Sequence navigator - 4v9j: Chain AA,CA
Sequence navigator - 4v9j: Chain AV,CV
Sequence navigator - 4v9j: Chain AW,CW
Sequence navigator - 4v9j: Chain AY,CY
Sequence navigator - 4v9j: Chain AU,CU
Sequence navigator - 4v9j: Chain BC,DC
Sequence navigator - 4v9j: Chain BD,DD
Sequence navigator - 4v9j: Chain BE,DE
Sequence navigator - 4v9j: Chain BF,DF
Sequence navigator - 4v9j: Chain BG,DG
Sequence navigator - 4v9j: Chain BH,DH
Sequence navigator - 4v9j: Chain BJ,DJ
Sequence navigator - 4v9j: Chain BK,DK
Sequence navigator - 4v9j: Chain BO,DO
Sequence navigator - 4v9j: Chain BP,DP
Sequence navigator - 4v9j: Chain BQ,DQ
Sequence navigator - 4v9j: Chain BR,DR
Sequence navigator - 4v9j: Chain BS,DS
Sequence navigator - 4v9j: Chain BT,DT
Sequence navigator - 4v9j: Chain BU,DU
Sequence navigator - 4v9j: Chain BV,DV
Sequence navigator - 4v9j: Chain BW,DW
Sequence navigator - 4v9j: Chain BX,DX
Sequence navigator - 4v9j: Chain BY,DY
Sequence navigator - 4v9j: Chain BZ,DZ
Sequence navigator - 4v9j: Chain B0,D0
Sequence navigator - 4v9j: Chain B1,D1
Sequence navigator - 4v9j: Chain B4,D4
Sequence navigator - 4v9j: Chain BN,DN
Sequence navigator - 4v9j: Chain B2,D2
Sequence navigator - 4v9j: Chain B3,D3
Sequence navigator - 4v9j: Chain B5,D5
Sequence navigator - 4v9j: Chain B6,D6
Sequence navigator - 4v9j: Chain B7,D7
Sequence navigator - 4v9j: Chain B8,D8
Sequence navigator - 4v9j: Chain B9,D9
Sequence navigator - 4v9j: Chain Be,De
Sequence navigator - 4v9j: Chain Bf,Bg,Df,Dg
Sequence navigator - 4v9j: Chain Bh,Dh
Sequence navigator - 4v9j: Chain BB,DB
Sequence navigator - 4v9j: Chain BA,DA

> Downloads

Resources

File formatFile name (file size)
PDB Bundle4v9j-pdb-bundle.tar.gz (5.95 MB)
PDBx/mmCIF4v9j.cif.gz (7.92 MB)
PDBMLall4v9j.xml.gz (11.69 MB)
no-atom4v9j-noatom.xml.gz (1.36 MB)
Display
ext-atom4v9j-extatom.xml.gz (7.03 MB)
PDBMLplusall4v9j-plus.xml.gz (11.7 MB)
no-atom4v9j-plus-noatom.xml.gz (1.38 MB)
Display
add only4v9j-add.xml.gz (12.06 KB)
Display
RDF4v9j.rdf.gz (2.26 MB)
Display
Structure factorsr4v9jsf.ent.gz (4.79 MB)
Biological unit (mmCIF format)4v9j-assembly1.cif.gz (4.13 MB) (AB,AC,AD,AE,AF,...)
*author defined assembly, 61 molecule(s) (61-meric)
Display
4v9j-assembly2.cif.gz (4.14 MB) (CB,CC,CD,CE,CF,...)
*author defined assembly, 61 molecule(s) (61-meric)
Display
Validation reportsPDF4v9j​_validation.pdf.gz (155.54 KB)
Display
PDF-full4v9j​_full​_validation.pdf.gz (155.46 KB)
Display
XML4v9j​_validation.xml.gz (613 B)
Display
Sequence (fasta)4v9j​_seq.txt
Display

PDBj@FacebookPDBj@TwitterwwPDBwwPDB FoundationEM DataBank

Copyright © 2013-2016 Protein Data Bank Japan