SAXSdb — 8rtd

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

TrwJ protein

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 34	TrwG protein × 12 （A8R756） TrwE protein × 3 （A8R758） TrwI protein × 5 （A8R754） TrwM protein × 3 （A8R750） Type IV secretion system protein virB4 × 6 （A8R751）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A8R752_SALDU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–229； UniProt 1–229 Author chain B； PDBConstruct 1–229； UniProt 1–229 Author chain C； PDBConstruct 1–229； UniProt 1–229 Author chain E； PDBConstruct 1–229； UniProt 1–229 Author chain K； PDBConstruct 1–229； UniProt 1–229

TrwG protein

Escherichia coli

UniProt A8R756

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 34	TrwJ protein × 5 （A8R752） TrwE protein × 3 （A8R758） TrwI protein × 5 （A8R754） TrwM protein × 3 （A8R750） Type IV secretion system protein virB4 × 6 （A8R751）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A8R756_SALDU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–231； UniProt 1–231 Author chain F； PDBConstruct 1–231； UniProt 1–231 Author chain G； PDBConstruct 1–231； UniProt 1–231 Author chain Q； PDBConstruct 1–231； UniProt 1–231 Author chain S； PDBConstruct 1–231； UniProt 1–231 Author chain U； PDBConstruct 1–231； UniProt 1–231 Author chain X； PDBConstruct 1–231； UniProt 1–231 Author chain Y； PDBConstruct 1–231； UniProt 1–231 Author chain b； PDBConstruct 1–231； UniProt 1–231 Author chain c； PDBConstruct 1–231； UniProt 1–231 Author chain d； PDBConstruct 1–231； UniProt 1–231 Author chain i； PDBConstruct 1–231； UniProt 1–231

TrwE protein

Escherichia coli

UniProt A8R758

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 34	TrwJ protein × 5 （A8R752） TrwG protein × 12 （A8R756） TrwI protein × 5 （A8R754） TrwM protein × 3 （A8R750） Type IV secretion system protein virB4 × 6 （A8R751）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A8R758_SALDU
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain Z； PDBConstruct 1–395； UniProt 1–395 Author chain a； PDBConstruct 1–395； UniProt 1–395 Author chain e； PDBConstruct 1–395； UniProt 1–395

TrwI protein

Escherichia coli

UniProt A8R754

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 34	TrwJ protein × 5 （A8R752） TrwG protein × 12 （A8R756） TrwE protein × 3 （A8R758） TrwM protein × 3 （A8R750） Type IV secretion system protein virB4 × 6 （A8R751）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A8R754_SALDU
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain H； PDBConstruct 1–342； UniProt 1–342 Author chain I； PDBConstruct 1–342； UniProt 1–342 Author chain J； PDBConstruct 1–342； UniProt 1–342 Author chain L； PDBConstruct 1–342； UniProt 1–342 Author chain M； PDBConstruct 1–342； UniProt 1–342

TrwM protein

Escherichia coli

UniProt A8R750

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 34	TrwJ protein × 5 （A8R752） TrwG protein × 12 （A8R756） TrwE protein × 3 （A8R758） TrwI protein × 5 （A8R754） Type IV secretion system protein virB4 × 6 （A8R751）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A8R750_SALDU
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain R； PDBConstruct 1–104； UniProt 1–104 Author chain f； PDBConstruct 1–104； UniProt 1–104 Author chain j； PDBConstruct 1–104； UniProt 1–104

Type IV secretion system protein virB4

Escherichia coli

UniProt A8R751

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 34	TrwJ protein × 5 （A8R752） TrwG protein × 12 （A8R756） TrwE protein × 3 （A8R758） TrwI protein × 5 （A8R754） TrwM protein × 3 （A8R750）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A8R751_SALDU
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain O； PDBConstruct 1–823； UniProt 1–823 Author chain P； PDBConstruct 1–823； UniProt 1–823 Author chain T； PDBConstruct 1–823； UniProt 1–823 Author chain V； PDBConstruct 1–823； UniProt 1–823 Author chain g； PDBConstruct 1–823； UniProt 1–823 Author chain h； PDBConstruct 1–823； UniProt 1–823

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	8rtd
Deposition date deposition_date	2024-01-25
Structure title title	Stalk-Arches-IMC structure from the fully-assembled R388 type IV secretion system determined by cryo-EM.
Keywords keywords	;type IV secretion system type 4 secretion system T4SS Arches Stalk inner membrane complex IMC R388 plasmid conjugation bacterial secretion secretion secretion system protein complex VirB3 VirB4 VirB5 VirB6 VirB8 VirB10 TrwM TrwK TrwJ TrwI TrwG TrwE, MEMBRANE PROTEIN ;; MEMBRANE PROTEIN
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.

8rtd__assembly_1__model_1

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

Download this curve (.dat)

8rtd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8rtd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	85.60 Å
Rg (electron density)	86.41 Å
Total Rg	86.38 Å
Atom count	40078
Residues	8254
Excluded volume	640500 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8rtd__assembly_1__model_1`	34-meric （34）	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 (6)

Entity 1 Entity 1 polymer

Description description	TrwJ protein
Molecular weight formula_weight	25190.5 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,K,E
Atom count atom_count	40078

MKKLVMTAAVAAILGAASPVMAQGIPVFDGTRALDFVQQFARMKEQLDTAKDQLAEAQRMYEAVTGGRGLGDLMRNAQLREYLPDDLRTVYDSANGGGYSGISGSINDILRDERLNGSVADMRRSIEERSRTAAATDKAVGLRAYEGAQQRLAQIEGLMDEISRTQDQKAIEELQARIAGEQAAIQNETTKLQMIAQLRQAEQALISEQRRERNMRILSSGNQGMPTIQ

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	TrwG protein
Molecular weight formula_weight	25800.0 kDa
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,F,G,Q,S,U,X,Y,b,c,d,i

MSKKQPKPVKAEQLKSYYEESRGLERDLIGEFVKSRKTAWRVATASGLFGLLGMVCGIVGFSQPAPAPLVLRVDNATGAVDVVTTLREHESSYGEVVDTYWLNQYVLNREAYDYNTIQMNYDTTALLSAPAVQQDYYKLFDGSNARDRVLGNKARITVRVRSIQPNGRGQATVRFTTQQHNSNGTVEAPQHQIATIGYTYIGAPMRSSDRLLNPLGFQVTSYRADPEILNN

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	TrwE protein
Molecular weight formula_weight	42443.8 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	a,Z,e

MFGRKKGDVIDAGAELERAEQERIEGEYGASELASERRPHTPGARTLLMVLLCVIAVVLVTLSYKAYKVRGVVEDDDAQPQQVVRQVIPGYTPRPIRPEPENVPEPPQPTTSVPAIQPAPVTQPVRPQPTGPREKTPYELARERMLRSGLTAGSGGGEDLPRPQGGDVPAGGLMGGGGGGGELAEKLQPMRLSGSSAGRLGNRDMLITQGTQLDCVLETRLVTTQPGMTTCHLTRDVYSTSGRVVLLDRGSKVVGFYQGGLRQGQARIFVQWSRIETPSGVVINLDSPGTGPLGEAGLGGWIDRHFWERFGGAIMISLIGDLGDWASRQGSRQGDNSIQFSNTANGVESAAAEALRNSINIPPTLYKNQGERVNILVARDLDFSDVYSLESIPTK

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	TrwI protein
Molecular weight formula_weight	35324.2 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,M,H,I,J

MAFELFTPLFNKIDQTTATYVTDISSRAIAAITPVVSVGLTLGFITYGWLIIRGAVEMPVAEFLNRCLRIGIIVSIALAGGLYQGEIANAITTVPDELASALLGNPTQGASAAALVDQSAQQGFDRASEAFEEAGFFSSDGLLYGLFGIIILLATGLLAAIGGAFLLLAKIALALLAGLGPLFILALIWQPTHRFFDQWAQQVLNYGLLIVLFAAVFGLLMQIFGSYMADLRFDGAQNVAYAIGGSVILSIVSIVLLMQLPSIASGLAGGIGLGYMWELRSMRSGAGAAMRGGRAMARGARAAPGAARGAAVGAANMAKTVATGGAGVARAAAGYFRGRKAG

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	TrwM protein
Molecular weight formula_weight	12292.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	j,R,f

MKPPQQQHEAFPLFKGATRLPTIWGVPMIPLMAMVMGVAVIALTVSIWWWALVPPLWFIMAQITKNDDKAFRIWWLWIDTKFRNRNKGFWGASSYSPANYRKRR

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	Type IV secretion system protein virB4
Molecular weight formula_weight	93769.9 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O,P,T,V,g,h

MGAIESRKLLASETPVGQFIPYSHHVTDTIISTKNAEYLSVWKIDGRSHQSASEADVFQWIRELNNTLRGISSANLSLWTHIVRRRVYEYPDAEFDNVFCRQLDEKYRESFTGYNLMVNDLYLTVVYRPVSDKVLSFFAKRERETPDQKKHRQESCIKALEDINRTLGQSFKRYGAELLSVYEKGGHAFSAPLEFLARLVNGEHIPMPICRDRFSDYMAVNRPMFSKWGEVGELRSLTGLRRFGMLEIREYDDATEPGQLNVLLESDYEFVLTHSFSVLSRPAAKEYLQRHQKNLIDARDVATDQIEEIDEALNQLISGHFVMGEHHCTLTVYGETVQQVRDNLAHASAAMLDVAVLPKPVDLALEAGYWAQLPANWQWRPRPAPITSLNFLSFSPFHNFMSGKPTGNPWGPAVTILKTVSGTPLYFNFHASKEEEDATDKRLLGNTMLIGQSSSGKTVLLGFLLAQAQKFKPTIVAFDKDRGMEISIRAMGGRYLPLKTGEPSGFNPFQLPPTHANLIFLKQFVKKLAAAGGEVTHRDEEEIDQAITAMMSDSIDKSLRRLSLLLQFLPNPRSDDMDARPTVHARLVKWCEGGDYGWLFDNPTDALDLSTHQIYGFDITEFLDNPEARTPVMMYLLYRTESMIDGRRFMYVFDEFWKPLQDEYFEDLAKNKQKTIRKQNGIFVFATQEPSDALESNIAKTLIQQCATYIFLANPKADYEDYTQGFKLTDSEFELVRGLGEFSRRFLIKQGDQSALAEMNLGKFRTIVDGETVERDFDDELLVLSGTPDNAEIAESIIAEVGDDPAVWLPIFLDRVKAERSDV

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

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Resolution resolution	4.33 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	65173

Stalk-Arches-IMC structure from the fully-assembled R388 type IV secretion system determined by cryo-EM.

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

TrwJ protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

TrwG protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

TrwE protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

TrwI protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

TrwM protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Type IV secretion system protein virB4

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

8rtd__assembly_1__model_1

8rtd__assembly_1__model_1 | I(q)

8rtd__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

7. Citations (1)