5A9Z image
Deposition Date 2015-07-23
Release Date 2015-10-14
Last Version Date 2024-10-16
Entry Detail
PDB ID:
5A9Z
Keywords:
RIBOSOME
Title:
Complex of Thermous thermophilus ribosome bound to BipA-GDPCP
Biological Source:
Source Organism:
Thermus thermophilus HB8 (Taxon ID: 300852)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
4.70 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
5A9Z validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:A (auth: AA)
Chain Length:71
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:B (auth: AB)
Chain Length:57
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L1
Chain IDs:C (auth: AC)
Chain Length:228
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SLP7 Pfam ID:PF00687
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Chain IDs:D (auth: AD)
Chain Length:272
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:P60405 Pfam ID:PF00181, PF03947
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Chain IDs:E (auth: AE)
Chain Length:206
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHN8 Pfam ID:PF00297
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:F (auth: AF)
Chain Length:37
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHN9 Pfam ID:PF00573
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:G (auth: AG)
Chain Length:182
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHQ0 Pfam ID:PF00281, PF00673
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Chain IDs:H (auth: AH)
Chain Length:174
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:P0DOY8 Pfam ID:PF00347
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L10
Chain IDs:I (auth: AI)
Chain Length:153
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:Q8VVE3 Pfam ID:PF00466
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Chain IDs:J (auth: AJ)
Chain Length:134
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SLP6 Pfam ID:PF03946, PF00298
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Chain IDs:K (auth: AK)
Chain Length:139
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:P60488 Pfam ID:PF00572
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Chain IDs:L (auth: AL)
Chain Length:122
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHP8 Pfam ID:PF00238
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Chain IDs:M (auth: AM)
Chain Length:145
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHQ7 Pfam ID:PF00828
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:N (auth: AN)
Chain Length:136
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:P60489 Pfam ID:PF00252
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Chain IDs:O (auth: AO)
Chain Length:117
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:Q9Z9H5 Pfam ID:PF01196
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Chain IDs:P (auth: AP)
Chain Length:110
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHQ4 Pfam ID:PF00861
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Chain IDs:Q (auth: AQ)
Chain Length:117
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:P60490 Pfam ID:PF01245
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Chain IDs:R (auth: AR)
Chain Length:117
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:P60491 Pfam ID:PF00453
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Chain IDs:S (auth: AS)
Chain Length:101
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:P60492 Pfam ID:PF00829
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Chain IDs:T (auth: AT)
Chain Length:110
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHP3 Pfam ID:PF00237
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Chain IDs:U (auth: AU)
Chain Length:94
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHP0 Pfam ID:PF00276
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Chain IDs:V (auth: AV)
Chain Length:110
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHP9 Pfam ID:PF00467, PF17136
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Chain IDs:W (auth: AW)
Chain Length:180
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHZ1 Pfam ID:PF01386, PF14693
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:X (auth: AX)
Chain Length:85
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:P60493 Pfam ID:PF01016
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Chain IDs:Y (auth: AY)
Chain Length:67
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHP6 Pfam ID:PF00831
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Chain IDs:Z (auth: AZ)
Chain Length:59
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHQ6 Pfam ID:PF00327
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Chain IDs:AA (auth: Aa)
Chain Length:71
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SJE1 Pfam ID:PF01197
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:BA (auth: Ab)
Chain Length:57
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:P80339 Pfam ID:PF01783
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Chain IDs:CA (auth: Ac)
Chain Length:228
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:P35871 Pfam ID:PF00471
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:DA (auth: Ad)
Chain Length:272
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:P80340 Pfam ID:PF00468
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Chain IDs:EA (auth: Ae)
Chain Length:206
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SKU1 Pfam ID:PF01632
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Chain IDs:FA (auth: Af)
Chain Length:37
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHR2 Pfam ID:PF00444
Polymer Type:polypeptide(L)
Molecule:Unknown peptide
Chain IDs:GA (auth: Ag)
Chain Length:182
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:HA (auth: BA)
Chain Length:1515
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Chain IDs:IA (auth: BF)
Chain Length:234
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:P80371 Pfam ID:PF00318
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Chain IDs:JA (auth: BG)
Chain Length:206
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:P80372 Pfam ID:PF07650, PF00189
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Chain IDs:KA (auth: BH)
Chain Length:208
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:P80373 Pfam ID:PF00163, PF01479
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Chain IDs:LA (auth: BI)
Chain Length:150
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHQ5 Pfam ID:PF00333, PF03719
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Chain IDs:MA (auth: BJ)
Chain Length:101
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SLP8 Pfam ID:PF01250
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Chain IDs:NA (auth: BK)
Chain Length:155
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:P17291 Pfam ID:PF00177
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Chain IDs:OA (auth: BL)
Chain Length:138
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:P0DOY9 Pfam ID:PF00410
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:PA (auth: BM)
Chain Length:127
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:P80374 Pfam ID:PF00380
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Chain IDs:QA (auth: BN)
Chain Length:98
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHN7 Pfam ID:PF00338
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Chain IDs:RA (auth: BO)
Chain Length:119
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:P80376 Pfam ID:PF00411
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Chain IDs:SA (auth: BP)
Chain Length:124
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHN3 Pfam ID:PF00164
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Chain IDs:TA (auth: BQ)
Chain Length:114
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:P80377 Pfam ID:PF00416
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14 type Z
Chain IDs:UA (auth: BR)
Chain Length:60
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:P0DOY6 Pfam ID:PF00253
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Chain IDs:VA (auth: BS)
Chain Length:88
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SJ76 Pfam ID:PF00312
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Chain IDs:WA (auth: BT)
Chain Length:83
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SJH3 Pfam ID:PF00886
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Chain IDs:XA (auth: BU)
Chain Length:104
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:P0DOY7 Pfam ID:PF00366
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Chain IDs:YA (auth: BV)
Chain Length:73
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SLQ0 Pfam ID:PF01084
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Chain IDs:ZA (auth: BW)
Chain Length:80
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SHP2 Pfam ID:PF00203
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:AB (auth: BX)
Chain Length:99
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:P80380 Pfam ID:PF01649
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein Thx
Chain IDs:BB (auth: BY)
Chain Length:24
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:Q5SIH3 Pfam ID:PF17070
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:BipA
Chain IDs:CB (auth: CA)
Chain Length:593
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
UniProt ID:P0A3B2 Pfam ID:PF00009, PF03144, PF00679, PF21018
Ligand Molecules
GCP
NMY
Primary Citation
Structure of Bipa in GTP Form Bound to the Ratcheted Ribosome.
Proc.Natl.Acad.Sci.USA 112 10944 10949 (2015)
PMID: 26283392 DOI: 10.1073/PNAS.1513216112

Abstact

BPI-inducible protein A (BipA) is a member of the family of ribosome-dependent translational GTPase (trGTPase) factors along with elongation factors G and 4 (EF-G and EF4). Despite being highly conserved in bacteria and playing a critical role in coordinating cellular responses to environmental changes, its structures (isolated and ribosome bound) remain elusive. Here, we present the crystal structures of apo form and GTP analog, GDP, and guanosine-3',5'-bisdiphosphate (ppGpp)-bound BipA. In addition to having a distinctive domain arrangement, the C-terminal domain of BipA has a unique fold. Furthermore, we report the cryo-electron microscopy structure of BipA bound to the ribosome in its active GTP form and elucidate the unique structural attributes of BipA interactions with the ribosome and A-site tRNA in the light of its possible function in regulating translation.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
5A9Z