OCA Atlas for 4V9I

4V9I

Crystal structure of thermus thermophilus 70S in complex with tRNAs and mRNA containing a pseudouridine in a stop codon

date

authors

Fernandez, I.S., Ng, C.L., Kelley, A.C., Guowei, W., Yu, Y.T., Ramakrishnan, V.

compound

source

symmetry

R_factor

R_Free

0.2785

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma

method

X-Ray Diffraction

resolution

3.30

note

4V9I supersedes 4K0L, 4K0M, 4K0P, 4K0Q

Gene
Ontology

Chain	Function	Process	Component
AB, CB
AC, CC
AH, CH
AI, CI
AL, CL
AM, CM
AN, CN
AO, CO
AS, CS
AT, CT
AU, CU
B0, D0
B1, D1
B3, D3
B4, D4
B6, D6
B7, D7
BC, DC
BE, DE
BF, DF
BN, DN
BO, DO
BQ, DQ
BS, DS
BT, DT
BW, DW
BX, DX
BY, DY
CD, AD
CE, AE
CF, AF
CG, AG
CJ, AJ
CK, AK
CP, AP
CQ, AQ
CR, AR
D2, B2
D5, B5
D8, B8
D9, B9
DD, BD
DG, BG
DH, BH
DI, BI
DJ, BJ
DP, BP
DR, BR
DU, BU
DV, BV
DZ, BZ

Primary reference

Unusual base pairing during the decoding of a stop codon by the ribosome., Fernandez IS, Ng CL, Kelley AC, Wu G, Yu YT, Ramakrishnan V, Nature. 2013 Jun 30. doi: 10.1038/nature12302. PMID:23812587

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1125 Kb) [Save to disk]

CSU: Contacts of Structural Units for 4V9I

Structure Factors (13367 Kb)

Retrieve 4V9I in mmCIF format [Save to disk]

View 4V9I in 3D

Proteopedia, because life has more than 2D.

On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.

On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 4V9I

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [4v9i_DP] [4v9i_BP] [4v9i_CC] [4v9i_AS] [4v9i_AJ] [4v9i_AA] [4v9i_AP] [4v9i_B8] [4v9i_DA] [4v9i_DY] [4v9i_D1] [4v9i_BS] [4v9i_AW] [4v9i_CJ] [4v9i_BQ] [4v9i_BF] [4v9i_BV] [4v9i_CQ] [4v9i_CY] [4v9i_CL] [4v9i_D7] [4v9i_AI] [4v9i_DG] [4v9i_AD] [4v9i_B2] [4v9i_CR] [4v9i_BR] [4v9i_AV] [4v9i_DD] [4v9i_DW] [4v9i_CF] [4v9i_DH] [4v9i_CP] [4v9i_BZ] [4v9i_CW] [4v9i_CO] [4v9i_DV] [4v9i_D5] [4v9i_DR] [4v9i_D6] [4v9i_AU] [4v9i_AX] [4v9i_BX] [4v9i_CI] [4v9i_BH] [4v9i_CS] [4v9i_DB] [4v9i_AF] [4v9i_BY] [4v9i_DS] [4v9i_AR] [4v9i_B5] [4v9i_CB] [4v9i_CE] [4v9i_BW] [4v9i_AY] [4v9i_CN] [4v9i_AQ] [4v9i_CT] [4v9i_B0] [4v9i_D4] [4v9i_BG] [4v9i_AE] [4v9i_DN] [4v9i_BJ] [4v9i_AH] [4v9i_B1] [4v9i_BU] [4v9i_BT] [4v9i_DF] [4v9i_B3] [4v9i_BI] [4v9i_CH] [4v9i_BE] [4v9i_CD] [4v9i_CM] [4v9i_B4] [4v9i_AC] [4v9i_D2] [4v9i_AG] [4v9i_DC] [4v9i_DO] [4v9i_B9] [4v9i_DT] [4v9i_BO] [4v9i_D0] [4v9i_BC] [4v9i_DX] [4v9i_AM] [4v9i_DU] [4v9i_BA] [4v9i] [4v9i_CK] [4v9i_CG] [4v9i_DZ] [4v9i_AN] [4v9i_CA] [4v9i_D9] [4v9i_CX] [4v9i_DJ] [4v9i_D3] [4v9i_B7] [4v9i_BB] [4v9i_AT] [4v9i_CU] [4v9i_AO] [4v9i_DI] [4v9i_BN] [4v9i_DQ] [4v9i_CV] [4v9i_AB] [4v9i_BD] [4v9i_B6] [4v9i_AL] [4v9i_DE] [4v9i_D8] [4v9i_AK]

SWISS-PROT database:

Domain organization of by SWISSPFAM

Domains found in 4V9I: [KH] [KOW] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART

Other resources with information on 4V9I

Community annotation for 4V9I at PDBWiki (http://pdbwiki.org)

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