4W2I

Crystal structure of the Thermus thermophilus 70S ribosome in complex with negamycin, mRNA and three deacylated tRNAs in the A, P and E sites

This is a large structure.

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
AA, CA16S Ribosomal RNApolymer1521493652.22
GenBank (AP008226.1)
Thermus thermophilus
AB, CB30S Ribosomal Protein S2polymer25629317.72
UniProt (P80371)
Pfam (PF00318)
Thermus thermophilus
AC, CC30S Ribosomal Protein S3polymer23926751.12
UniProt (P80372)
Pfam (PF00189)
Pfam (PF07650)
Thermus thermophilus
AD, CD30S Ribosomal Protein S4polymer20924373.42
UniProt (P80373)
Pfam (PF00163)
Pfam (PF01479)
Thermus thermophilus
AE, CE30S Ribosomal Protein S5polymer16217583.42
UniProt (Q5SHQ5)
Pfam (PF00333)
Pfam (PF03719)
Thermus thermophilus
AF, CF30S Ribosomal Protein S6polymer10111988.82
UniProt (Q5SLP8)
Pfam (PF01250)
Thermus thermophilus
AG, CG30S Ribosomal Protein S7polymer15618051.02
UniProt (P17291)
Pfam (PF00177)
Thermus thermophilus
AH, CH30S Ribosomal Protein S8polymer13815868.62
UniProt (Q5SHQ2)
Pfam (PF00410)
UniProt (by SIFTS) (A0A0M9AFS9)
Thermus thermophilus
AI, CI30S Ribosomal Protein S9polymer12814410.62
UniProt (P80374)
Pfam (PF00380)
Thermus thermophilus
AJ, CJ30S Ribosomal Protein S10polymer10511955.02
UniProt (Q5SHN7)
Pfam (PF00338)
Thermus thermophilus
AK, CK30S Ribosomal Protein S11polymer12913737.92
UniProt (P80376)
Pfam (PF00411)
Thermus thermophilus
AL, CL30S Ribosomal Protein S12polymer13214637.42
UniProt (Q5SHN3)
Pfam (PF00164)
Thermus thermophilus
AM, CM30S Ribosomal Protein S13polymer12614338.92
UniProt (P80377)
Pfam (PF00416)
Thermus thermophilus
AN, CN30S Ribosomal Protein S14polymer617158.72
UniProt (Q5SHQ1)
Pfam (PF00253)
UniProt (by SIFTS) (A0A0N0BLP2)
Thermus thermophilus
AO, CO30S Ribosomal Protein S15polymer8910578.42
UniProt (Q5SJ76)
Pfam (PF00312)
Thermus thermophilus
AP, CP30S Ribosomal Protein S16polymer8810410.02
UniProt (Q5SJH3)
Pfam (PF00886)
Thermus thermophilus
AQ, CQ30S Ribosomal Protein S17polymer10512325.72
UniProt (Q5SHP7)
Pfam (PF00366)
UniProt (by SIFTS) (P0DOY7)
Thermus thermophilus
AR, CR30S Ribosomal Protein S18polymer8810258.32
UniProt (Q5SLQ0)
Pfam (PF01084)
Thermus thermophilus
AS, CS30S Ribosomal Protein S19polymer9310605.52
UniProt (Q5SHP2)
Pfam (PF00203)
Thermus thermophilus
AT, CT30S Ribosomal Protein S20polymer10611736.12
UniProt (P80380)
Pfam (PF01649)
Thermus thermophilus
AU, CU30S Ribosomal Protein THXpolymer273350.02
UniProt (Q5SIH3)
Pfam (PF17070)
Thermus thermophilus
AV, CVmRNApolymer247804.72
synthetic construct
AW, AY, CW, CYA/P-site tRNApolymer7624647.94
Escherichia coli@PDBj
AX, CXE-site tRNApolymer7724846.92
Escherichia coli@PDBj
BA, DA23S Ribosomal RNApolymer2915947895.42
GenBank (AP008226.1)
Thermus thermophilus
BB, DB5S Ribosomal RNApolymer12139188.42
GenBank (AP008226.1|)
Thermus thermophilus
BD, DD50S Ribosomal Protein L2polymer27630532.62
UniProt (P60405)
Pfam (PF00181)
Pfam (PF03947)
Thermus thermophilus
BE, DE50S Ribosomal Protein L3polymer20622450.22
UniProt (Q5SHN8)
Pfam (PF00297)
Thermus thermophilus
BF, DF50S Ribosomal Protein L4polymer21023271.92
UniProt (Q5SHN9)
Pfam (PF00573)
Thermus thermophilus
BG, DG50S Ribosomal Protein L5polymer18221061.62
UniProt (Q5SHQ0)
Pfam (PF00281)
Pfam (PF00673)
Thermus thermophilus
BH, DH50S Ribosomal Protein L6polymer18019568.92
UniProt (Q5SHQ3)
Pfam (PF00347)
UniProt (by SIFTS) (A0A0M9ADP1)
Thermus thermophilus
BI, DI50S Ribosomal Protein L9polymer14816422.22
UniProt (Q5SLQ1)
Pfam (PF01281)
Pfam (PF03948)
Thermus thermophilus
BN, DN50S Ribosomal Protein L13polymer14015927.92
UniProt (P60488)
Pfam (PF00572)
Thermus thermophilus
BO, DO50S Ribosomal Protein L14polymer12213323.62
UniProt (Q5SHP8)
Pfam (PF00238)
Thermus thermophilus
BP, DP50S Ribosomal Protein L15polymer15016319.12
UniProt (Q5SHQ7)
Pfam (PF00828)
Thermus thermophilus
BQ, DQ50S Ribosomal Protein L16polymer14115993.92
UniProt (P60489)
Pfam (PF00252)
Thermus thermophilus
BR, DR50S Ribosomal Protein L17polymer11813750.12
UniProt (Q9Z9H5)
Pfam (PF01196)
Thermus thermophilus
BS, DS50S Ribosomal Protein L18polymer11212639.82
UniProt (Q5SHQ4)
Pfam (PF00861)
Thermus thermophilus
BT, DT50S Ribosomal Protein L19polymer14617188.82
UniProt (P60490)
Pfam (PF01245)
Thermus thermophilus
BU, DU50S Ribosomal Protein L20polymer11813779.32
UniProt (P60491)
Pfam (PF00453)
Thermus thermophilus
BV, DV50S Ribosomal Protein L21polymer10111069.22
UniProt (P60492)
Pfam (PF00829)
Thermus thermophilus
BW, DW50S Ribosomal Protein L22polymer11312808.12
UniProt (Q5SHP3)
Pfam (PF00237)
Thermus thermophilus
BX, DX50S Ribosomal Protein L23polymer9610759.82
UniProt (Q5SHP0)
Pfam (PF00276)
Thermus thermophilus
BY, DY50S Ribosomal Protein L24polymer11012085.62
UniProt (Q5SHP9)
Pfam (PF00467)
Pfam (PF17136)
Thermus thermophilus
BZ, DZ50S Ribosomal Protein L25polymer20623238.62
UniProt (Q5SHZ1)
Pfam (PF01386)
Pfam (PF14693)
Thermus thermophilus
B0, D050S Ribosomal Protein L27polymer859529.12
UniProt (P60493)
Pfam (PF01016)
Thermus thermophilus
B1, D150S Ribosomal Protein L28polymer9811004.22
UniProt (P60494)
Pfam (PF00830)
Thermus thermophilus
B2, D250S Ribosomal Protein L29polymer728670.32
UniProt (Q5SHP6)
Pfam (PF00831)
Thermus thermophilus
B3, D350S Ribosomal Protein L30polymer606799.12
UniProt (Q5SHQ6)
Pfam (PF00327)
Thermus thermophilus
B4, D450S Ribosomal Protein L31polymer718300.52
UniProt (Q5SJE1)
Pfam (PF01197)
Thermus thermophilus
B5, D550S Ribosomal Protein L32polymer606722.12
UniProt (P80339)
Pfam (PF01783)
Thermus thermophilus
B6, D650S Ribosomal Protein L33polymer546632.92
UniProt (P35871)
Pfam (PF00471)
Thermus thermophilus
B7, D750S Ribosomal Protein L34polymer496132.42
UniProt (P80340)
Pfam (PF00468)
Thermus thermophilus
B8, D850S Ribosomal Protein L35polymer657506.22
UniProt (Q5SKU1)
Pfam (PF01632)
Thermus thermophilus
B9, D950S Ribosomal Protein L36polymer374435.42
UniProt (Q5SHR2)
Pfam (PF00444)
Thermus thermophilus
MAGNESIUM IONnon-polymer24.32013
NEGAMYCINnon-polymer248.319
IRON/SULFUR CLUSTERnon-polymer351.62
ZINC IONnon-polymer65.412
POTASSIUM IONnon-polymer39.12
waterwater18.03049

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains112
Total molecular weight4500086.1
Non-Polymers*Number of molecules2048
Total molecular weight55209.7
All*Total molecular weight4555295.8
*Water molecules are not included.