National Center for
Biotechnology Information

4V6D: Crystal structure of the E. coli 70S ribosome in an intermediate state of ratcheting

PDB ID:

4V6D Download

MMDB ID:

171007

PDB Deposition Date:

2009/6/27

Updated in MMDB:

2024/11

Experimental Method:

x-ray diffraction

Resolution:

3.814 Å

Source Organism:

Escherichia coli K-12▼

Taxonomy	Molecule
Escherichia coli K-12	AB, AC, AD, AE, AF, AG, AH, AI, AJ, AK, AL, AM, AN, AO, AP, AQ, AR, AS, AT, AU, BC, BD, BE, BF, BG, BH, BI, BJ, BK, BL, BM, BN, BO, BP, BQ, BR, BS, BT, BU, BV, BW, BX, BY, BZ, B0, B1, B2, B3, B4, CB, CC, CD, CE, CF, CG, CH, CI, CJ, CK, CL, CM, CN, CO, CP, CQ, CR, CS, CT, CU, DC, DD, DE, DF, DG, DH, DI, DJ, DK, DL, DM, DN, DO, DP, DQ, DR, DS, DT, DU, DV, DW, DX, DY, DZ, D0, D1, D2, D3, D4
synthetic construct	AV, AW, CV, CW
Escherichia coli	AA, BA, BB, CA, DA, DB

Similar Structures:

Entry 3I1Q is obsolete, it has been replaced with 4V6D.

Asymmetric Unit for 4V6D: 54-meric; determined by author

Molecular Components in 4V6D
Label	Count	Molecule
Proteins (49 molecules)
AB	1	30S Ribosomal Protein S2
AC	1	30S Ribosomal Protein S3
AD	1	30S Ribosomal Protein S4
AE	1	30S Ribosomal Protein S5
AF	1	30S Ribosomal Protein S6
AG	1	30S Ribosomal Protein S7
AH	1	30S Ribosomal Protein S8
AI	1	30S Ribosomal Protein S9
AJ	1	30S Ribosomal Protein S10
AK	1	30S Ribosomal Protein S11
AL	1	30S Ribosomal Protein S12
AM	1	30S Ribosomal Protein S13
AN	1	30S Ribosomal Protein S14
AO	1	30S Ribosomal Protein S15
AP	1	30S Ribosomal Protein S16
AQ	1	30S Ribosomal Protein S17
AR	1	30S Ribosomal Protein S18
AS	1	30S Ribosomal Protein S19
AT	1	30S Ribosomal Protein S20
AU	1	30S Ribosomal Protein S21
BC	1	50S Ribosomal Protein L2
BD	1	50S Ribosomal Protein L3
BE	1	50S Ribosomal Protein L4
BF	1	50S Ribosomal Protein L5
BG	1	50S Ribosomal Protein L6
BH	1	50S Ribosomal Protein L9
BI	1	50S Ribosomal Protein L11
BJ	1	50S Ribosomal Protein L13
BK	1	50S Ribosomal Protein L14
BL	1	50S Ribosomal Protein L15
BM	1	50S Ribosomal Protein L16
BN	1	50S Ribosomal Protein L17
BO	1	50S Ribosomal Protein L18
BP	1	50S Ribosomal Protein L19
BQ	1	50S Ribosomal Protein L20
BR	1	50S Ribosomal Protein L21
BS	1	50S Ribosomal Protein L22
BT	1	50S Ribosomal Protein L23
BU	1	50S Ribosomal Protein L24
BV	1	50S Ribosomal Protein L25
BW	1	50S Ribosomal Protein L27
BX	1	50S Ribosomal Protein L28
BY	1	50S Ribosomal Protein L29
BZ	1	50S Ribosomal Protein L30
B0	1	50S Ribosomal Protein L32
B1	1	50S Ribosomal Protein L33
B2	1	50S Ribosomal Protein L34
B3	1	50S Ribosomal Protein L35
B4	1	50S Ribosomal Protein L36
Nucleotides(5 molecules)
AA	1	16S rRNA
AV	1	P-site tRNA ASL Fragment
AW	1	Messenger RNA
BA	1	23S rRNA
BB	1	5S rRNA
Chemicals and Non-standard biopolymers (155 molecules)
1	154	MAGNESIUM ION
2	1	ZINC ION

* Click molecule labels to explore molecular sequence information.

Citing MMDB

Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303