SAXSdb — 6gyb

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

VirB7

Xanthomonas axonopodis pv. citri (strain 306)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 42	VirB9 protein × 14 （Q8PJB5） VirB10 protein × 14 （Q8PJB6）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8PJB3_XANAC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–139； UniProt 1–139 Author chain D； PDBConstruct 1–139； UniProt 1–139 Author chain G； PDBConstruct 1–139； UniProt 1–139 Author chain J； PDBConstruct 1–139； UniProt 1–139 Author chain M； PDBConstruct 1–139； UniProt 1–139 Author chain P； PDBConstruct 1–139； UniProt 1–139 Author chain S； PDBConstruct 1–139； UniProt 1–139 Author chain a； PDBConstruct 1–139； UniProt 1–139 Author chain d； PDBConstruct 1–139； UniProt 1–139 Author chain g； PDBConstruct 1–139； UniProt 1–139 Author chain j； PDBConstruct 1–139； UniProt 1–139 Author chain m； PDBConstruct 1–139； UniProt 1–139 Author chain p； PDBConstruct 1–139； UniProt 1–139 Author chain s； PDBConstruct 1–139； UniProt 1–139

VirB9 protein

Xanthomonas axonopodis pv. citri (strain 306)

UniProt Q8PJB5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 42	VirB7 × 14 （Q8PJB3） VirB10 protein × 14 （Q8PJB6）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8PJB5_XANAC
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–255； UniProt 1–255 Author chain E； PDBConstruct 1–255； UniProt 1–255 Author chain H； PDBConstruct 1–255； UniProt 1–255 Author chain K； PDBConstruct 1–255； UniProt 1–255 Author chain N； PDBConstruct 1–255； UniProt 1–255 Author chain Q； PDBConstruct 1–255； UniProt 1–255 Author chain T； PDBConstruct 1–255； UniProt 1–255 Author chain b； PDBConstruct 1–255； UniProt 1–255 Author chain e； PDBConstruct 1–255； UniProt 1–255 Author chain h； PDBConstruct 1–255； UniProt 1–255 Author chain k； PDBConstruct 1–255； UniProt 1–255 Author chain n； PDBConstruct 1–255； UniProt 1–255 Author chain q； PDBConstruct 1–255； UniProt 1–255 Author chain t； PDBConstruct 1–255； UniProt 1–255

VirB10 protein

Xanthomonas axonopodis pv. citri (strain 306)

UniProt Q8PJB6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 42	VirB7 × 14 （Q8PJB3） VirB9 protein × 14 （Q8PJB5）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8PJB6_XANAC
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–389； UniProt 1–389 Author chain F； PDBConstruct 1–389； UniProt 1–389 Author chain I； PDBConstruct 1–389； UniProt 1–389 Author chain L； PDBConstruct 1–389； UniProt 1–389 Author chain O； PDBConstruct 1–389； UniProt 1–389 Author chain R； PDBConstruct 1–389； UniProt 1–389 Author chain U； PDBConstruct 1–389； UniProt 1–389 Author chain c； PDBConstruct 1–389； UniProt 1–389 Author chain f； PDBConstruct 1–389； UniProt 1–389 Author chain i； PDBConstruct 1–389； UniProt 1–389 Author chain l； PDBConstruct 1–389； UniProt 1–389 Author chain o； PDBConstruct 1–389； UniProt 1–389 Author chain r； PDBConstruct 1–389； UniProt 1–389 Author chain u； PDBConstruct 1–389； UniProt 1–389

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	6gyb
Deposition date deposition_date	2018-06-28
Structure title title	Cryo-EM structure of the bacteria-killing type IV secretion system core complex from Xanthomonas citri
Keywords keywords	core complex, bacterial killing, protein transport, bacterial Type IV Secretion System, 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.

6gyb__assembly_1__model_1

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

Download this curve (.dat)

6gyb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6gyb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	73.67 Å
Rg (electron density)	73.38 Å
Total Rg	73.46 Å
Atom count	59318
Residues	7546
Excluded volume	1056200 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6gyb__assembly_1__model_1`	42-meric （42）	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 (3)

Entity 1 Entity 1 polymer

Description description	VirB7
Molecular weight formula_weight	14762.8 kDa
Source method src_method	man
Copy count entity_count	14

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	a,d,g,j,m,p,s,A,D,G,J,M,P,S
Atom count atom_count	59318

MNPMYVSKLSLVLVAAALVGACATKPAPDFGGRWKHVNHFDEAPTEIPLYTSYTYQATPMDGTLKTMLERWAADSNMQLSYNLPSDYTLIGPVSAISTTSVQQAATELSAVYAAQGVSVSVSANKLLVQPVPVSSGAKL

Source Source

Source organism organism	Xanthomonas axonopodis pv. citri (strain 306)
NCBI taxonomy ID ncbi_taxonomy_id	190486
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	VirB9 protein
Molecular weight formula_weight	29359.4 kDa
Source method src_method	man
Copy count entity_count	14

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	b,e,h,k,n,q,t,B,E,H,K,N,Q,T

MKLFNRYRVALLSALPLALCALSAAAQVVQEYEYAPDRIYQVRTGLGITTQVELSPNEKILDYSTGFTGGWELTRRENVFYLKPKNVDVDTNMMIRTATHSYILELKVVATDWQRLEQAKQAGVQYKVVFTYPKDTSFNNVADADTSKNGPLLNAKILKDRRYYYDYDYATRTKKSWLIPSRVYDDGKFTYINMDLTRFPTGNFPAVFAREKEHAEDFLVNTTVEGNTLIVHGTYPFLVVRHGDNVVGLRRNKQK

Source Source

Source organism organism	Xanthomonas axonopodis pv. citri (strain 306)
NCBI taxonomy ID ncbi_taxonomy_id	190486
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	VirB10 protein
Molecular weight formula_weight	43392.5 kDa
Source method src_method	man
Copy count entity_count	14

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	c,f,i,l,o,r,u,C,F,I,L,O,R,U

MNSNIPNSPDERIQNHGGDEQHNGDHNERNNPYFARQQASAEPDLDANEPILRSSDIKRLNRKALVFLAAIAALLILAIFWLATQSGEDSAPPKPRTETVVAPALPQSMTAPVEEAPVPLAQQPSLPPLPPMPTDNSEEVSSAPERQRGPTLLERRILAESAANGGGVPGQLGAQPAPTQEDGPVTLAKPISNPDGLLVRGTYIRCILETRIISDFGGYTSCIVTEPVYSINGHNLLLPKGSKMLGQYSAGEPTSHRLQVVWDRVTTPTGLDVTLMGPGIDTLGSSGHPGNYNAHWGNKIASALFISLLSDAFKYAAAEYGPETTTIGVGSGIVTQQPFESNTARSMQQLAEQAVEKSGRRPATLTINQGTVLNVYVAKDVDFSAVLPKAAALEGLSAWSHPQFEK

Source Source

Source organism organism	Xanthomonas axonopodis pv. citri (strain 306)
NCBI taxonomy ID ncbi_taxonomy_id	190486
Host organism host_organism	Escherichia coli BL21(DE3)

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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	1

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

Resolution resolution	3.28 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	142306

Cryo-EM structure of the bacteria-killing type IV secretion system core complex from Xanthomonas citri

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

VirB7

State in the Current Structure

Other States of the Same Protein in the Database

VirB9 protein

State in the Current Structure

Other States of the Same Protein in the Database

VirB10 protein

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6gyb__assembly_1__model_1

6gyb__assembly_1__model_1 | I(q)

6gyb__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 (3)

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

7. Citations (1)

Cryo-EM structure of the bacteria-killing type IV secretion system core complex from Xanthomonas citri

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

VirB7

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

VirB9 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

VirB10 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6gyb__assembly_1__model_1

6gyb__assembly_1__model_1 | I(q)

6gyb__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 (3)

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

7. Citations (1)