8cvo

Cutibacterium acnes 30S ribosomal subunit with Sarecycline bound, head domain only in the local refined map

Method: ELECTRON MICROSCOPY

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1. Protein Identity and Related Structures Protein Identity & Related Structures

30S ribosomal protein S5

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 8 RNA 1	16S ribosomal RNA × 1 30S ribosomal protein S3 × 1 （A0A2B7I5Y3） 30S ribosomal protein S7 × 1 （A0A2B7ITZ4） 30S ribosomal protein S9 × 1 （A0A2B7JN42） 30S ribosomal protein S10 × 1 （A0A085B5E4） 30S ribosomal protein S13 × 1 （A0A2C6LKT6） 30S ribosomal protein S14 type Z × 1 （A0A2B7JMX1） 30S ribosomal protein S19 × 1 （A0A2B7ITR7） Sarecycline × 1 MAGNESIUM ION × 12 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A2B7I5L8_CUTAC
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–215； UniProt 1–215

30S ribosomal protein S3

OrganismNot specified

UniProt A0A2B7I5Y3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 8 RNA 1	16S ribosomal RNA × 1 30S ribosomal protein S5 × 1 （A0A2B7I5L8） 30S ribosomal protein S7 × 1 （A0A2B7ITZ4） 30S ribosomal protein S9 × 1 （A0A2B7JN42） 30S ribosomal protein S10 × 1 （A0A085B5E4） 30S ribosomal protein S13 × 1 （A0A2C6LKT6） 30S ribosomal protein S14 type Z × 1 （A0A2B7JMX1） 30S ribosomal protein S19 × 1 （A0A2B7ITR7） Sarecycline × 1 MAGNESIUM ION × 12 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A2B7I5Y3_CUTAC
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain G； PDBConstruct 1–269； UniProt 1–269

30S ribosomal protein S7

OrganismNot specified

UniProt A0A2B7ITZ4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 8 RNA 1	16S ribosomal RNA × 1 30S ribosomal protein S5 × 1 （A0A2B7I5L8） 30S ribosomal protein S3 × 1 （A0A2B7I5Y3） 30S ribosomal protein S9 × 1 （A0A2B7JN42） 30S ribosomal protein S10 × 1 （A0A085B5E4） 30S ribosomal protein S13 × 1 （A0A2C6LKT6） 30S ribosomal protein S14 type Z × 1 （A0A2B7JMX1） 30S ribosomal protein S19 × 1 （A0A2B7ITR7） Sarecycline × 1 MAGNESIUM ION × 12 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A2B7ITZ4_CUTAC
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain I； PDBConstruct 1–156； UniProt 1–156

30S ribosomal protein S9

OrganismNot specified

UniProt A0A2B7JN42

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 8 RNA 1	16S ribosomal RNA × 1 30S ribosomal protein S5 × 1 （A0A2B7I5L8） 30S ribosomal protein S3 × 1 （A0A2B7I5Y3） 30S ribosomal protein S7 × 1 （A0A2B7ITZ4） 30S ribosomal protein S10 × 1 （A0A085B5E4） 30S ribosomal protein S13 × 1 （A0A2C6LKT6） 30S ribosomal protein S14 type Z × 1 （A0A2B7JMX1） 30S ribosomal protein S19 × 1 （A0A2B7ITR7） Sarecycline × 1 MAGNESIUM ION × 12 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A2B7JN42_CUTAC
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain J； PDBConstruct 1–173； UniProt 1–173

30S ribosomal protein S10

OrganismNot specified

UniProt A0A085B5E4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 8 RNA 1	16S ribosomal RNA × 1 30S ribosomal protein S5 × 1 （A0A2B7I5L8） 30S ribosomal protein S3 × 1 （A0A2B7I5Y3） 30S ribosomal protein S7 × 1 （A0A2B7ITZ4） 30S ribosomal protein S9 × 1 （A0A2B7JN42） 30S ribosomal protein S13 × 1 （A0A2C6LKT6） 30S ribosomal protein S14 type Z × 1 （A0A2B7JMX1） 30S ribosomal protein S19 × 1 （A0A2B7ITR7） Sarecycline × 1 MAGNESIUM ION × 12 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A085B5E4_CUTAC
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain M； PDBConstruct 1–103； UniProt 1–103

30S ribosomal protein S13

OrganismNot specified

UniProt A0A2C6LKT6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 8 RNA 1	16S ribosomal RNA × 1 30S ribosomal protein S5 × 1 （A0A2B7I5L8） 30S ribosomal protein S3 × 1 （A0A2B7I5Y3） 30S ribosomal protein S7 × 1 （A0A2B7ITZ4） 30S ribosomal protein S9 × 1 （A0A2B7JN42） 30S ribosomal protein S10 × 1 （A0A085B5E4） 30S ribosomal protein S14 type Z × 1 （A0A2B7JMX1） 30S ribosomal protein S19 × 1 （A0A2B7ITR7） Sarecycline × 1 MAGNESIUM ION × 12 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A2C6LKT6_CUTAC
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain N； PDBConstruct 1–123； UniProt 1–123

30S ribosomal protein S14 type Z

OrganismNot specified

UniProt A0A2B7JMX1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 8 RNA 1	16S ribosomal RNA × 1 30S ribosomal protein S5 × 1 （A0A2B7I5L8） 30S ribosomal protein S3 × 1 （A0A2B7I5Y3） 30S ribosomal protein S7 × 1 （A0A2B7ITZ4） 30S ribosomal protein S9 × 1 （A0A2B7JN42） 30S ribosomal protein S10 × 1 （A0A085B5E4） 30S ribosomal protein S13 × 1 （A0A2C6LKT6） 30S ribosomal protein S19 × 1 （A0A2B7ITR7） Sarecycline × 1 MAGNESIUM ION × 12 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A2B7JMX1_CUTAC
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain S； PDBConstruct 1–61； UniProt 1–61

30S ribosomal protein S19

OrganismNot specified

UniProt A0A2B7ITR7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 8 RNA 1	16S ribosomal RNA × 1 30S ribosomal protein S5 × 1 （A0A2B7I5L8） 30S ribosomal protein S3 × 1 （A0A2B7I5Y3） 30S ribosomal protein S7 × 1 （A0A2B7ITZ4） 30S ribosomal protein S9 × 1 （A0A2B7JN42） 30S ribosomal protein S10 × 1 （A0A085B5E4） 30S ribosomal protein S13 × 1 （A0A2C6LKT6） 30S ribosomal protein S14 type Z × 1 （A0A2B7JMX1） Sarecycline × 1 MAGNESIUM ION × 12 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A2B7ITR7_CUTAC
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain U； PDBConstruct 1–93； UniProt 1–93

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8cvo
Deposition date deposition_date	2022-05-18
Structure title title	Cutibacterium acnes 30S ribosomal subunit with Sarecycline bound, head domain only in the local refined map
Keywords keywords	ribosome, sarecycline, acne, ANTIBIOTIC; ANTIBIOTIC
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

8cvo__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8cvo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8cvo__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	39.55 Å
Rg (electron density)	39.64 Å
Total Rg	39.88 Å
Atom count	17421
Residues	1400
Excluded volume	273080 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8cvo__assembly_1__model_1`	nonameric （9）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (12)

Entity 1 Entity 1 polymer

Description description	16S ribosomal RNA
Molecular weight formula_weight	498742.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	A
Atom count atom_count	17421

UUUUUCAUUGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGGAAAGGCCCUGCUUUUGUGGGGUGCUCGAGUGGCGAACGGGUGAGUAACACGUGAGUAACCUGCCCUUGACUUUGGGAUAACUUCAGGAAACUGGGGCUAAUACCGGAUAGGAGCUCCUGCUGCAUGGUGGGGGUUGGAAAGUUUCGGCGGUUGGGGAUGGACUCGCGGCUUAUCAGCUUGUUGGUGGGGUAGUGGCUUACCAAGGCUUUGACGGGUAGCCGGCCUGAGAGGGUGACCGGCCACAUUGGGACUGAGAUACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGGAAGCCUGAUGCAGCAACGCCGCGUGCGGGAUGACGGCCUUCGGGUUGUAAACCGCUUUCGCCUGUGACGAAGCGUGAGUGACGGUAAUGGGUAAAGAAGCACCGGCUAACUACGUGCCAGCAGCCGCGGUGAUACGUAGGGUGCGAGCGUUGUCCGGAUUUAUUGGGCGUAAAGGGCUCGUAGGUGGUUGAUCGCGUCGGAAGUGUAAUCUUGGGGCUUAACCCUGAGCGUGCUUUCGAUACGGGUUGACUUGAGGAAGGUAGGGGAGAAUGGAAUUCCUGGUGGAGCGGUGGAAUGCGCAGAUAUCAGGAGGAACACCAGUGGCGAAGGCGGUUCUCUGGGCCUUUCCUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGCUUAGAUACCCUGGUAGUCCACGCUGUAAACGGUGGGUACUAGGUGUGGGGUCCAUUCCACGGGUUCCGUGCCGUAGCUAACGCUUUAAGUACCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGCCCCGCACAAGCGGCGGAGCAUGCGGAUUAAUUCGAUGCAACGCGUAGAACCUUACCUGGGUUUGACAUGGAUCGGGAGUGCUCAGAGAUGGGUGUGCCUCUUUUGGGGUCGGUUCACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUCACUGUUGCCAGCACGUUAUGGUGGGGACUCAGUGGAGACCGCCGGGGUCAACUCGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGCCCCUUAUGUCCAGGGCUUCACGCAUGCUACAAUGGCUGGUACAGAGAGUGGCGAGCCUGUGAGGGUGAGCGAAUCUCGGAAAGCCGGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCUCAUGAAGUCGGAGUCGCUAGUAAUCGCAGAUCAGCAACGCUGCGGUGAAUACGUUCCCGGGGCUUGUACACACCGCCCGUCAAGUCAUGAAAGUUGGUAACACCCGAAGCCGGUGGCCUAACCGUUGUGGGGGAGCCGUCGAAGGUGGGACUGGUGAUUAGGACUAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCUAAGGAG

Entity 2 Entity 2 polymer

Description description	30S ribosomal protein S5
Molecular weight formula_weight	22603.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MSGTQRRGGGAGGERRGRDNRRGQNDRNRNQNEYLERVVAINRVAKVVQGGRRFSFTALVVVGDGEGSVGVGYGKAKEVPAAIAKAVEEAKKHFFKVPLVGRTITHPVIGEKAAGVVMLRPASPGTGVIAGGSARAVLECAGVHDVLAKSLGSSNAINVVHATVDALQQLEEPEEVARRRGKSVEDIAPAAMLRARKEADEAAAAARMEEKAGVN

Entity 3 Entity 3 polymer

Description description	30S ribosomal protein S3
Molecular weight formula_weight	29728.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MGQKINPHGFRLGVTTDHKTRWYAEKQYAELVGEDVKIREWLHKNLERAGLSSIEIERRSERVTIFLYAARPGIVIGRNGAEAERVRGELEKLTGKQIQLNILEVKSPETDAQLVAQGIAEQLAARVAFRRAMRKAQQSAMNAGALGIRIKCSGRLGGAEMSRSEGYREGRVPLHTLRADIDYGFFEARTTFGRIGVKVWIYKGDVTGTRAERAAQKAARQAAQGGRGGRGGNRRGRGDRPDRRGGRRRAEAAKQSAETPAPQTENAGA

Entity 4 Entity 4 polymer

Description description	30S ribosomal protein S7
Molecular weight formula_weight	17615.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

MPRKGPAPKRPVMVDPVYGSPLVSQLVSKILLDGKKTVAQNIVYTALEGCRAKNNTDPVQTLKRALDNIKPSLEVKSRRVGGATYQVPVEVKPARQTTLAMRWLVNFSRERREKTMAERLMNEILDASNGLGASVKRREDTHKMAEANRAFAHYRW

Entity 5 Entity 5 polymer

Description description	30S ribosomal protein S9
Molecular weight formula_weight	18630.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

MTDTPTENLENTEVTPFTEGDREIAYRTDSNPTVAAGDSKRPAMIAPGAATGRRKEAIARVRITPGSGQWKINGRTLEDYFPNKVHQQIVTEPFATAGVEGAYDVIARIGGGGVTGQAGALRLGIARALNNVDPEASRPALKKAGMLTRDARVKERKKAGLKKARKAPQYSKR

Entity 6 Entity 6 polymer

Description description	30S ribosomal protein S10
Molecular weight formula_weight	11750.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

MAGQKIRIRLRAYDHEVIDSSARKIVDTVTRTGAKVAGPVPLPTEKNVFCVIRSPHKYKDSREHFEMRTHKRLIDILEPTPKTVDSLMRLDLPAGVDIEIKLP

Entity 7 Entity 7 polymer

Description description	30S ribosomal protein S13
Molecular weight formula_weight	14030.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N

MARLIGVDLPRDKRLEVALTYIYGIGRTRATETLKATGISGDLRVHELTDDQLVALRDHIEANYHVEGDLRREVAADIRRKIEIGTYQGRRHRSGLPVRGQRTRTNARTRKGKRKAVAKKKAK

Entity 8 Entity 8 polymer

Description description	30S ribosomal protein S14 type Z
Molecular weight formula_weight	6924.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	S

MAKTALKVKAARKPKFGVRAYTRCQRCGRPHSVYRKFGLCRICLREMAHAGQLPGVTKSSW

Entity 9 Entity 9 polymer

Description description	30S ribosomal protein S19
Molecular weight formula_weight	10536.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U

MPRSLKKGPFVDEHLAKKVTAQNEAGTHNVIKTWSRRSMVTPDMIGHTIGVHDGRKHVPVFVTESMVGHKLGEFAPTRTFKGHVKDDKKARRR

Entity 10 Entity 10 non-polymer

Description description	Sarecycline
Molecular weight formula_weight	487.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 12 Entity 12 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	8cvoI01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	455 — Ribosomal Protein S7
Homologous superfamily homologous superfamily	10 — Ribosomal protein S7/S5

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.95 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	70853

Cutibacterium acnes 30S ribosomal subunit with Sarecycline bound, head domain only in the local refined map

1. Protein Identity and Related Structures Protein Identity & Related Structures

30S ribosomal protein S5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

30S ribosomal protein S3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

30S ribosomal protein S7

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

30S ribosomal protein S9

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

30S ribosomal protein S10

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

30S ribosomal protein S13

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

30S ribosomal protein S14 type Z

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

30S ribosomal protein S19

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8cvo__assembly_1__model_1

8cvo__assembly_1__model_1 | I(q)

8cvo__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (12)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer