8cgi

Pentacycline TP038 bound to the 30S head

Method: ELECTRON MICROSCOPY

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

Large ribosomal subunit protein bL31A

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 rRNA × 1 Small ribosomal subunit protein uS3 × 1 （P0A7V3） 30S ribosomal protein S7 × 1 （P02359） Small ribosomal subunit protein uS9 × 1 （P0A7X3） Small ribosomal subunit protein uS10 × 1 （P0A7R5） Small ribosomal subunit protein uS13 × 1 （P0A7S9） Small ribosomal subunit protein uS14 × 1 （P0AG59） Small ribosomal subunit protein uS19 × 1 （P0A7U3） Pentacycline × 1 POTASSIUM ION × 10 MAGNESIUM ION × 32 water × 9	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL31_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain 4； PDBConstruct 1–70； UniProt 1–70

Small ribosomal subunit protein uS3

OrganismNot specified

UniProt P0A7V3

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	Large ribosomal subunit protein bL31A × 1 （P0A7M9） 16S rRNA × 1 30S ribosomal protein S7 × 1 （P02359） Small ribosomal subunit protein uS9 × 1 （P0A7X3） Small ribosomal subunit protein uS10 × 1 （P0A7R5） Small ribosomal subunit protein uS13 × 1 （P0A7S9） Small ribosomal subunit protein uS14 × 1 （P0AG59） Small ribosomal subunit protein uS19 × 1 （P0A7U3） Pentacycline × 1 POTASSIUM ION × 10 MAGNESIUM ION × 32 water × 9	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS3_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–233； UniProt 1–233

30S ribosomal protein S7

OrganismNot specified

UniProt P02359

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	Large ribosomal subunit protein bL31A × 1 （P0A7M9） 16S rRNA × 1 Small ribosomal subunit protein uS3 × 1 （P0A7V3） Small ribosomal subunit protein uS9 × 1 （P0A7X3） Small ribosomal subunit protein uS10 × 1 （P0A7R5） Small ribosomal subunit protein uS13 × 1 （P0A7S9） Small ribosomal subunit protein uS14 × 1 （P0AG59） Small ribosomal subunit protein uS19 × 1 （P0A7U3） Pentacycline × 1 POTASSIUM ION × 10 MAGNESIUM ION × 32 water × 9	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS7_ECOLI
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain G； PDBConstruct 1–179； UniProt 1–179

Small ribosomal subunit protein uS9

OrganismNot specified

UniProt P0A7X3

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	Large ribosomal subunit protein bL31A × 1 （P0A7M9） 16S rRNA × 1 Small ribosomal subunit protein uS3 × 1 （P0A7V3） 30S ribosomal protein S7 × 1 （P02359） Small ribosomal subunit protein uS10 × 1 （P0A7R5） Small ribosomal subunit protein uS13 × 1 （P0A7S9） Small ribosomal subunit protein uS14 × 1 （P0AG59） Small ribosomal subunit protein uS19 × 1 （P0A7U3） Pentacycline × 1 POTASSIUM ION × 10 MAGNESIUM ION × 32 water × 9	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS9_ECOLI
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain I； PDBConstruct 1–130； UniProt 1–130

Small ribosomal subunit protein uS10

OrganismNot specified

UniProt P0A7R5

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	Large ribosomal subunit protein bL31A × 1 （P0A7M9） 16S rRNA × 1 Small ribosomal subunit protein uS3 × 1 （P0A7V3） 30S ribosomal protein S7 × 1 （P02359） Small ribosomal subunit protein uS9 × 1 （P0A7X3） Small ribosomal subunit protein uS13 × 1 （P0A7S9） Small ribosomal subunit protein uS14 × 1 （P0AG59） Small ribosomal subunit protein uS19 × 1 （P0A7U3） Pentacycline × 1 POTASSIUM ION × 10 MAGNESIUM ION × 32 water × 9	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS10_ECOLI
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain J； PDBConstruct 1–103； UniProt 1–103

Small ribosomal subunit protein uS13

OrganismNot specified

UniProt P0A7S9

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	Large ribosomal subunit protein bL31A × 1 （P0A7M9） 16S rRNA × 1 Small ribosomal subunit protein uS3 × 1 （P0A7V3） 30S ribosomal protein S7 × 1 （P02359） Small ribosomal subunit protein uS9 × 1 （P0A7X3） Small ribosomal subunit protein uS10 × 1 （P0A7R5） Small ribosomal subunit protein uS14 × 1 （P0AG59） Small ribosomal subunit protein uS19 × 1 （P0A7U3） Pentacycline × 1 POTASSIUM ION × 10 MAGNESIUM ION × 32 water × 9	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS13_ECOLI
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain M； PDBConstruct 1–118； UniProt 1–118

Small ribosomal subunit protein uS14

OrganismNot specified

UniProt P0AG59

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	Large ribosomal subunit protein bL31A × 1 （P0A7M9） 16S rRNA × 1 Small ribosomal subunit protein uS3 × 1 （P0A7V3） 30S ribosomal protein S7 × 1 （P02359） Small ribosomal subunit protein uS9 × 1 （P0A7X3） Small ribosomal subunit protein uS10 × 1 （P0A7R5） Small ribosomal subunit protein uS13 × 1 （P0A7S9） Small ribosomal subunit protein uS19 × 1 （P0A7U3） Pentacycline × 1 POTASSIUM ION × 10 MAGNESIUM ION × 32 water × 9	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS14_ECOLI
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain N； PDBConstruct 1–101； UniProt 1–101

Small ribosomal subunit protein uS19

OrganismNot specified

UniProt P0A7U3

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	Large ribosomal subunit protein bL31A × 1 （P0A7M9） 16S rRNA × 1 Small ribosomal subunit protein uS3 × 1 （P0A7V3） 30S ribosomal protein S7 × 1 （P02359） Small ribosomal subunit protein uS9 × 1 （P0A7X3） Small ribosomal subunit protein uS10 × 1 （P0A7R5） Small ribosomal subunit protein uS13 × 1 （P0A7S9） Small ribosomal subunit protein uS14 × 1 （P0AG59） Pentacycline × 1 POTASSIUM ION × 10 MAGNESIUM ION × 32 water × 9	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS19_ECOLI
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain S； PDBConstruct 1–92； UniProt 1–92

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	8cgi
Deposition date deposition_date	2023-02-04
Structure title title	Pentacycline TP038 bound to the 30S head
Keywords keywords	Antibiotic, RIBOSOME; RIBOSOME
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.

8cgi__assembly_1__model_1

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

Download this curve (.dat)

8cgi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8cgi__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.85 Å
Rg (electron density)	38.60 Å
Total Rg	38.92 Å
Atom count	16605
Residues	1298
Excluded volume	260800 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8cgi__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 (13)

Entity 1 Entity 1 polymer

Description description	Large ribosomal subunit protein bL31A
Molecular weight formula_weight	7887.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	4
Atom count atom_count	17553

MKKDIHPKYEEITASCSCGNVMKIRSTVGHDLNLDVCSKCHPFFTGKQRDVATGGRVDRFNKRFNIPGSK

Entity 2 Entity 2 polymer

Description description	16S rRNA
Molecular weight formula_weight	499197.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	A

AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGCCCUUCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUGACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCCUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGAAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCU

Entity 3 Entity 3 polymer

Description description	Small ribosomal subunit protein uS3
Molecular weight formula_weight	26031.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERPAKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSITSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRADIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK

Entity 4 Entity 4 polymer

Description description	30S ribosomal protein S7
Molecular weight formula_weight	20055.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MPRRRVIGQRKILPDPKFGSELLAKFVNILMVDGKKSTAESIVYSALETLAQRSGKSELEAFEVALENVRPTVEVKSRRVGGSTYQVPVEVRPVRRNALAMRWIVEAARKRGDKSMALRLANELSDAAENKGTAVKKREDVHRMAEANKAFAHYRWLSLRSFSHQAGASSKQPALGYLN

Entity 5 Entity 5 polymer

Description description	Small ribosomal subunit protein uS9
Molecular weight formula_weight	14886.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

MAENQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEKLDLYITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRKARRRPQFSKR

Entity 6 Entity 6 polymer

Description description	Small ribosomal subunit protein uS10
Molecular weight formula_weight	11755.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

MQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKDARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISLG

Entity 7 Entity 7 polymer

Description description	Small ribosomal subunit protein uS13
Molecular weight formula_weight	13128.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

MARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVAKFVVEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRGQRTKTNARTRKGPRKPIKK

Entity 8 Entity 8 polymer

Description description	Small ribosomal subunit protein uS14
Molecular weight formula_weight	11606.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N

MAKQSMKAREVKRVALADKYFAKRAELKAIISDVNASDEDRWNAVLKLQTLPRDSSPSRQRNRCRQTGRPHGFLRKFGLSRIKVREAAMRGEIPGLKKASW

Entity 9 Entity 9 polymer

Description description	Small ribosomal subunit protein uS19
Molecular weight formula_weight	10455.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	S

MPRSLKKGPFIDLHLLKKVEKAVESGDKKPLRTWSRRSTIFPNMIGLTIAVHNGRQHVPVFVTDEMVGHKLGEFAPTRTYRGHAADKKAKKK

Entity 10 Entity 10 non-polymer

Description description	Pentacycline
Molecular weight formula_weight	551.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 12 Entity 12 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	32

Entity 13 Entity 13 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	948

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	8cgiG01
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

Domain ID domain_id	8cgiM01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	50 —

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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	1.890 Å
Low-resolution limit resolution_low	137.770 Å
R factor r_factor	0.2612
R_work r_work	0.2612
R_free r_free	—

Resolution resolution	1.89 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	1301160

Pentacycline TP038 bound to the 30S head

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

Large ribosomal subunit protein bL31A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Small ribosomal subunit protein uS3

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

Small ribosomal subunit protein uS9

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Small ribosomal subunit protein uS10

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Small ribosomal subunit protein uS13

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Small ribosomal subunit protein uS14

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Small ribosomal subunit protein uS19

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

8cgi__assembly_1__model_1

8cgi__assembly_1__model_1 | I(q)

8cgi__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (13)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer