SAXSdb — 2vx8

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

NUCLEOPORIN-LIKE PROTEIN RIP, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7

MUS MUSCULUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2	CHLORIDE ION × 2 water × 2	Consistent with protein count
2	Insufficient information	Monomer	Protein 1	water × 1	Consistent with protein count
3	Insufficient information	Monomer	Protein 1	CHLORIDE ION × 2 water × 1	Consistent with protein count
4	Insufficient information	Monomer	Protein 1	water × 1	Consistent with protein count
5	Insufficient information	Monomer	Protein 1	CHLORIDE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NUPL_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–42； UniProt 136–175 Author chain B； PDBConstruct 3–42； UniProt 136–175 Author chain C； PDBConstruct 3–42； UniProt 136–175 Author chain D； PDBConstruct 3–42； UniProt 136–175

NUCLEOPORIN-LIKE PROTEIN RIP, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7

MUS MUSCULUS

UniProt P70280

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2	CHLORIDE ION × 2 water × 2	Consistent with protein count
2	Insufficient information	Monomer	Protein 1	water × 1	Consistent with protein count
3	Insufficient information	Monomer	Protein 1	CHLORIDE ION × 2 water × 1	Consistent with protein count
4	Insufficient information	Monomer	Protein 1	water × 1	Consistent with protein count
5	Insufficient information	Monomer	Protein 1	CHLORIDE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VAMP7_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 44–163； UniProt 1–120 Author chain B； PDBConstruct 44–163； UniProt 1–120 Author chain C； PDBConstruct 44–163； UniProt 1–120 Author chain D； PDBConstruct 44–163； UniProt 1–120

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	2vx8
Deposition date deposition_date	2008-07-01
Structure title title	Vamp7 longin domain Hrb peptide complex
Keywords keywords	;ENDOCYTOSIS, EXOCYTOSIS, MEMBRANE PROTEIN, SIGNAL-ANCHOR, SNARE, MEMBRANE, ENDOSOME, LYSOSOME, TRANSPORT, CYTOPLASMIC VESICLE, ENDOPLASMIC RETICULUM, PROTEIN TRANSPORT, VESICLE TRANSPORT, TRANSMEMBRANE, GOLGI APPARATUS, CLATHRIN ADAPTOR ;; ENDOCYTOSIS,EXOCYTOSIS
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.

2vx8__assembly_1__model_1

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

Download this curve (.dat)

2vx8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vx8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.52 Å
Rg (electron density)	21.68 Å
Total Rg	22.59 Å
Atom count	2154
Residues	274
Excluded volume	38518 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vx8__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2vx8__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2vx8__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2vx8__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2vx8__assembly_5__model_1`	monomeric （1）	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	NUCLEOPORIN-LIKE PROTEIN RIP, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7
Molecular weight formula_weight	18681.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4418

GSVASVHASISGSSASSTSSTPEVKPLKSLLGDSAPTLHLNKGMAILFAVVARGTTILAKHAWCGGNFLEVTEQILAKIPSENNKLTYSHGNYLFHYICQDRIVYLCITDDDFERSRAFSFLNEVKKRFQTTYGSRAQTALPYAMNSEFSSVLAAQLKHHSENHHHHHH

Source Source

Source organism organism	MUS MUSCULUS
Common name common_name	MOUSE
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	170

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2vx8A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	50 — Longin domain

Domain ID domain_id	2vx8B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	50 — Longin domain

Domain ID domain_id	2vx8C00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	50 — Longin domain

Domain ID domain_id	2vx8D00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	50 — Longin domain

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Unit-cell length a length_a	105.514 Å
Unit-cell length b length_b	115.102 Å
Unit-cell length c length_c	55.440 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	16

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	57.710 Å
R factor r_factor	0.2230
R_work r_work	0.2200
R_free r_free	0.2800

Vamp7 longin domain Hrb peptide complex

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

NUCLEOPORIN-LIKE PROTEIN RIP, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7

State in the Current Structure

Other States of the Same Protein in the Database

NUCLEOPORIN-LIKE PROTEIN RIP, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7

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

2vx8__assembly_1__model_1

2vx8__assembly_1__model_1 | I(q)

2vx8__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Vamp7 longin domain Hrb peptide complex

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

NUCLEOPORIN-LIKE PROTEIN RIP, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

NUCLEOPORIN-LIKE PROTEIN RIP, VESICLE-ASSOCIATED MEMBRANE PROTEIN 7

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

2vx8__assembly_1__model_1

2vx8__assembly_1__model_1 | I(q)

2vx8__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)