8ZFF image
Deposition Date 2024-05-07
Release Date 2025-11-12
Last Version Date 2025-11-12
Entry Detail
PDB ID:
8ZFF
Keywords:
RIBOSOME
Title:
Structure of the Bacterial Ribosome without hypoxia-induced rRNA modifications
Biological Source:
Source Organism:
Escherichia phage T4 (Taxon ID: 2681598)
Escherichia coli BW25113 (Taxon ID: 679895)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.59 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8ZFF validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL33
Gene (Uniprot):rpmG
Chain IDs:VA (auth: 0)
Chain Length:55
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7N9 Pfam ID:PF00471
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL34
Gene (Uniprot):rpmH
Chain IDs:WA (auth: 1)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7P5 Pfam ID:PF00468
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL35
Gene (Uniprot):rpmI
Chain IDs:XA (auth: 2)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7Q1 Pfam ID:PF01632
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL36A
Gene (Uniprot):rpmJ
Chain IDs:YA (auth: 3)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7Q6 Pfam ID:PF00444
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL31
Gene (Uniprot):rpmE
Chain IDs:ZA (auth: 4)
Chain Length:70
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7M9 Pfam ID:PF01197
Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:A
Chain Length:2904
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS2
Gene (Uniprot):rpsB
Chain IDs:B
Chain Length:241
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7V0 Pfam ID:PF00318
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS3
Gene (Uniprot):rpsC
Chain IDs:C
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7V3 Pfam ID:PF07650, PF00189
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS4
Gene (Uniprot):rpsD
Chain IDs:D
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7V8 Pfam ID:PF00163, PF01479
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS5
Gene (Uniprot):rpsE
Chain IDs:E
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7W1 Pfam ID:PF00333, PF03719
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS6, fully modified isoform
Gene (Uniprot):rpsF
Chain IDs:F
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P02358 Pfam ID:PF01250
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS7
Gene (Uniprot):rpsG
Chain IDs:G
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P02359 Pfam ID:PF00177
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS8
Gene (Uniprot):rpsH
Chain IDs:H
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7W7 Pfam ID:PF00410
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS9
Gene (Uniprot):rpsI
Chain IDs:I
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7X3 Pfam ID:PF00380
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS10
Gene (Uniprot):rpsJ
Chain IDs:J
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7R5 Pfam ID:PF00338
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS11
Gene (Uniprot):rpsK
Chain IDs:K
Chain Length:129
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7R9 Pfam ID:PF00411
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS12
Gene (Uniprot):rpsL
Chain IDs:L
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7S3 Pfam ID:PF00164
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS13
Gene (Uniprot):rpsM
Chain IDs:M
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7S9 Pfam ID:PF00416
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS14
Gene (Uniprot):rpsN
Chain IDs:N
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0AG59 Pfam ID:PF00253
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS15
Gene (Uniprot):rpsO
Chain IDs:O
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0ADZ4 Pfam ID:PF00312
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS16
Gene (Uniprot):rpsP
Chain IDs:P
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7T3 Pfam ID:PF00886
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS17
Gene (Uniprot):rpsQ
Chain IDs:Q
Chain Length:84
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0AG63 Pfam ID:PF00366
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS18
Gene (Uniprot):rpsR
Chain IDs:R
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7T7 Pfam ID:PF01084
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS19
Gene (Uniprot):rpsS
Chain IDs:S
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7U3 Pfam ID:PF00203
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS20
Gene (Uniprot):rpsT
Chain IDs:T
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7U7 Pfam ID:PF01649
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS21
Gene (Uniprot):rpsU
Chain IDs:U
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P68679 Pfam ID:PF01165
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:AB (auth: X)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia phage T4
Polymer Type:polyribonucleotide
Molecule:P-site tRNA-fMet
Chain IDs:BB (auth: Z)
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:V (auth: a)
Chain Length:2904
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:W (auth: b)
Chain Length:241
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL2
Gene (Uniprot):rplB
Chain IDs:X (auth: c)
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P60422 Pfam ID:PF00181, PF03947
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL3
Gene (Uniprot):rplC
Chain IDs:Y (auth: d)
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P60438 Pfam ID:PF00297
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL4
Gene (Uniprot):rplD
Chain IDs:Z (auth: e)
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P60723 Pfam ID:PF00573
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL5
Gene (Uniprot):rplE
Chain IDs:AA (auth: f)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P62399 Pfam ID:PF00281, PF00673
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL6
Gene (Uniprot):rplF
Chain IDs:BA (auth: g)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0AG55 Pfam ID:PF00347
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL9
Gene (Uniprot):rplI
Chain IDs:CA (auth: h)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7R1 Pfam ID:PF01281, PF03948
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL13
Gene (Uniprot):rplM
Chain IDs:DA (auth: i)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0AA10 Pfam ID:PF00572
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL14
Gene (Uniprot):rplN
Chain IDs:EA (auth: j)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0ADY3 Pfam ID:PF00238
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL15
Gene (Uniprot):rplO
Chain IDs:FA (auth: k)
Chain Length:129
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P02413 Pfam ID:PF00828
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL16
Gene (Uniprot):rplP
Chain IDs:GA (auth: l)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0ADY7 Pfam ID:PF00252
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL17
Gene (Uniprot):rplQ
Chain IDs:HA (auth: m)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0AG44 Pfam ID:PF01196
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL18
Gene (Uniprot):rplR
Chain IDs:IA (auth: n)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0C018 Pfam ID:PF00861
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL19
Gene (Uniprot):rplS
Chain IDs:JA (auth: o)
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7K6 Pfam ID:PF01245
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL20
Gene (Uniprot):rplT
Chain IDs:KA (auth: p)
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7L3 Pfam ID:PF00453
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL21
Gene (Uniprot):rplU
Chain IDs:LA (auth: q)
Chain Length:84
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0AG48 Pfam ID:PF00829
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL22
Gene (Uniprot):rplV
Chain IDs:MA (auth: r)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P61175 Pfam ID:PF00237
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL23
Gene (Uniprot):rplW
Chain IDs:NA (auth: s)
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0ADZ0 Pfam ID:PF00276
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL24
Gene (Uniprot):rplX
Chain IDs:OA (auth: t)
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P60624 Pfam ID:PF00467, PF17136
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL25
Gene (Uniprot):rplY
Chain IDs:PA (auth: u)
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P68919 Pfam ID:PF01386
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL27
Gene (Uniprot):rpmA
Chain IDs:QA (auth: v)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7L8 Pfam ID:PF01016
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL28
Gene (Uniprot):rpmB
Chain IDs:RA (auth: w)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7M2 Pfam ID:PF00830
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL29
Gene (Uniprot):rpmC
Chain IDs:SA (auth: x)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7M6 Pfam ID:PF00831
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL30
Gene (Uniprot):rpmD
Chain IDs:TA (auth: y)
Chain Length:59
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0AG51 Pfam ID:PF00327
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL32
Gene (Uniprot):rpmF
Chain IDs:UA (auth: z)
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7N4 Pfam ID:PF01783
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
2MG A G modified residue
4D4 GA ARG modified residue
4OC A C modified residue
4SU BB U modified residue
5MC A C modified residue
5MU BB U modified residue
D2T L ASP modified residue
G7M A G modified residue
H2U BB U modified residue
MA6 A A modified residue
MEQ Y GLN modified residue
OMC BB C modified residue
PSU A U modified residue
UR3 A U modified residue
Ligand Molecules
MG
Primary Citation
Novel rRNA methylations regulate translational efficiency of the ribosomes in response to oxygen condition
To Be Published ? ? ? (?)
Primary Citation of related structures
8ZFF
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