3cfi

Nanobody-aided structure determination of the EPSI:EPSJ pseudopilin heterdimer from Vibrio Vulnificus

Method: X-RAY DIFFRACTION

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

Type II secretory pathway, pseudopilin EpsI

Vibrio vulnificus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Type II secretory pathway, PSEUDOPILIN EpsJ × 1 （Q7MPZ0） Nanobody NBEPSIJ_11 × 1 CHLORIDE ION × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Type II secretory pathway, PSEUDOPILIN EpsJ × 1 （Q7MPZ0） Nanobody NBEPSIJ_11 × 1 CHLORIDE ION × 1 water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Type II secretory pathway, PSEUDOPILIN EpsJ × 1 （Q7MPZ0） Nanobody NBEPSIJ_11 × 1 CHLORIDE ION × 1 water × 3	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	Type II secretory pathway, PSEUDOPILIN EpsJ × 1 （Q7MPZ0） Nanobody NBEPSIJ_11 × 1 CHLORIDE ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7MPZ1_VIBVY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–84； UniProt 61–144 Author chain D； PDBConstruct 1–84； UniProt 61–144 Author chain G； PDBConstruct 1–84； UniProt 61–144 Author chain J； PDBConstruct 1–84； UniProt 61–144

Type II secretory pathway, PSEUDOPILIN EpsJ

Vibrio vulnificus

UniProt Q7MPZ0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Type II secretory pathway, pseudopilin EpsI × 1 （Q7MPZ1） Nanobody NBEPSIJ_11 × 1 CHLORIDE ION × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Type II secretory pathway, pseudopilin EpsI × 1 （Q7MPZ1） Nanobody NBEPSIJ_11 × 1 CHLORIDE ION × 1 water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Type II secretory pathway, pseudopilin EpsI × 1 （Q7MPZ1） Nanobody NBEPSIJ_11 × 1 CHLORIDE ION × 1 water × 3	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	Type II secretory pathway, pseudopilin EpsI × 1 （Q7MPZ1） Nanobody NBEPSIJ_11 × 1 CHLORIDE ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7MPZ0_VIBVY
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–164； UniProt 47–210 Author chain E； PDBConstruct 1–164； UniProt 47–210 Author chain H； PDBConstruct 1–164； UniProt 47–210 Author chain K； PDBConstruct 1–164； UniProt 47–210

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	3cfi
Deposition date deposition_date	2008-03-03
Structure title title	Nanobody-aided structure determination of the EPSI:EPSJ pseudopilin heterdimer from Vibrio Vulnificus
Keywords keywords	General Secretory Pathway, Pseudopilins, Single Chain Antibody, Methylation, PROTEIN TRANSPORT-Immune system COMPLEX; PROTEIN TRANSPORT/Immune system
Experimental Method method	X-RAY DIFFRACTION

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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.

3cfi__assembly_1__model_1

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

Download this curve (.dat)

3cfi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3cfi__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.69 Å
Rg (electron density)	24.28 Å
Total Rg	25.09 Å
Atom count	2789
Residues	351
Excluded volume	49410 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3cfi__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3cfi__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3cfi__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3cfi__assembly_4__model_1`	trimeric （3）	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 (5)

Entity 1 Entity 1 polymer

Description description	Type II secretory pathway, pseudopilin EpsI
Molecular weight formula_weight	9226.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,G,J
Atom count atom_count	11229

INTVGYLEQKMFAAMVADNQMAMVMLNPKNLKASNGEEELAGQTWYWKVAPVATTQPLLKAFDVSVAAEKQASPIITVRSYVAK

Source Source

Source organism organism	Vibrio vulnificus
NCBI taxonomy ID ncbi_taxonomy_id	672
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Type II secretory pathway, PSEUDOPILIN EpsJ
Molecular weight formula_weight	19203.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E,H,K

NELSQERTARLNELQRALVMMDSDFRQIALRQTRTNGEEPSKKLLHWADYLLDSDNKGIMFARLGWHNPQQQFPRGEVTKVGYRIKDERLERVWWRYPDTPAGQEGVVTPLLSDVEELNVRFYDGKQWINEWSNELTLPAAISVELTLKDYGKIARTYLTPEGN

Source Source

Source organism organism	Vibrio vulnificus
NCBI taxonomy ID ncbi_taxonomy_id	672
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Nanobody NBEPSIJ_11
Molecular weight formula_weight	12614.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F,I,L

QVQLQESGGGLVQPGGSLRLSCAASGFAFSGYAMSWVRQAPGKGLEWVSGINRDGSTSYTAPVKGRFTISRDNAKNILYLQMNSLRPEDTAVYYCAKWLGGRDWYDRGQGTQVTVS

Source Source

Source organism organism	Lama glama
NCBI taxonomy ID ncbi_taxonomy_id	9844
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	155

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d3cfia_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.24 — Pili subunits
Superfamily Superfamily superfamily	d.24.1 — Pili subunits
Family Family family	d.24.1.7 — GSPII I/J protein-like

Domain ID domain_id	d3cfib_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.24 — Pili subunits
Superfamily Superfamily superfamily	d.24.1 — Pili subunits
Family Family family	d.24.1.5 — EpsJ-like

Domain ID domain_id	d3cfic1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d3cfic2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3cfid_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.24 — Pili subunits
Superfamily Superfamily superfamily	d.24.1 — Pili subunits
Family Family family	d.24.1.7 — GSPII I/J protein-like

Domain ID domain_id	d3cfie_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.24 — Pili subunits
Superfamily Superfamily superfamily	d.24.1 — Pili subunits
Family Family family	d.24.1.5 — EpsJ-like

Domain ID domain_id	d3cfif1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d3cfif2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3cfig_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.24 — Pili subunits
Superfamily Superfamily superfamily	d.24.1 — Pili subunits
Family Family family	d.24.1.7 — GSPII I/J protein-like

Domain ID domain_id	d3cfih_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.24 — Pili subunits
Superfamily Superfamily superfamily	d.24.1 — Pili subunits
Family Family family	d.24.1.5 — EpsJ-like

Domain ID domain_id	d3cfii1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d3cfii2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3cfij_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.24 — Pili subunits
Superfamily Superfamily superfamily	d.24.1 — Pili subunits
Family Family family	d.24.1.7 — GSPII I/J protein-like

Domain ID domain_id	d3cfik_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.24 — Pili subunits
Superfamily Superfamily superfamily	d.24.1 — Pili subunits
Family Family family	d.24.1.5 — EpsJ-like

Domain ID domain_id	d3cfil1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d3cfil2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (8 domains)

Domain ID domain_id	3cfiA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1300 — Pantoate--beta-alanine Ligase; Chain: A,domain 2
Homologous superfamily homologous superfamily	30 — GSPII I/J protein-like

Domain ID domain_id	3cfiC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3cfiD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1300 — Pantoate--beta-alanine Ligase; Chain: A,domain 2
Homologous superfamily homologous superfamily	30 — GSPII I/J protein-like

Domain ID domain_id	3cfiF00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3cfiG00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1300 — Pantoate--beta-alanine Ligase; Chain: A,domain 2
Homologous superfamily homologous superfamily	30 — GSPII I/J protein-like

Domain ID domain_id	3cfiI00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3cfiJ00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1300 — Pantoate--beta-alanine Ligase; Chain: A,domain 2
Homologous superfamily homologous superfamily	30 — GSPII I/J protein-like

Domain ID domain_id	3cfiL00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	46.720 Å
Unit-cell length b length_b	67.243 Å
Unit-cell length c length_c	128.255 Å
Unit-cell angle α angle_alpha	96.54 °
Unit-cell angle β angle_beta	91.62 °
Unit-cell angle γ angle_gamma	90.20 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.580 Å
Low-resolution limit resolution_low	19.970 Å
R factor r_factor	0.2319
R_work r_work	0.2294
R_free r_free	0.2790

Nanobody-aided structure determination of the EPSI:EPSJ pseudopilin heterdimer from Vibrio Vulnificus

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

Type II secretory pathway, pseudopilin EpsI

State in the Current Structure

Other States of the Same Protein in the Database

Type II secretory pathway, PSEUDOPILIN EpsJ

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

3cfi__assembly_1__model_1

3cfi__assembly_1__model_1 | I(q)

3cfi__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (16 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Nanobody-aided structure determination of the EPSI:EPSJ pseudopilin heterdimer from Vibrio Vulnificus

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

Type II secretory pathway, pseudopilin EpsI

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 II secretory pathway, PSEUDOPILIN EpsJ

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

3cfi__assembly_1__model_1

3cfi__assembly_1__model_1 | I(q)

3cfi__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (16 domains)

CATH v4.4 (8 domains)

7. Citations (1)