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3vi3

Crystal structure of alpha5beta1 integrin headpiece (ligand-free form)

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Integrin alpha-5

Homo sapiens

UniProt P08648

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 4 其他Polymer 2 Integrin beta-1 × 1 （P05556） SG/19 Fab fragment (Light chain) × 1 SG/19 Fab fragment (Heavy chain) × 1 ;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 6 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 MAGNESIUM ION × 1 Consistent with protein count
2 Other combination Heteromer Protein 4 其他Polymer 2 Integrin beta-1 × 1 （P05556） SG/19 Fab fragment (Light chain) × 1 SG/19 Fab fragment (Heavy chain) × 1 ;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 6 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 MAGNESIUM ION × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
9hmh

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3vi3 3vi3 3vi4 3vi4 4wjk 4wk0 4wk2 4wk4 7nwl 7nxd 9b9j 9b9k

17 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name ITA5_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–623； UniProt 42–664 Author chain C； PDBConstruct 1–623； UniProt 42–664

Integrin beta-1

Homo sapiens

UniProt P05556

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 4 其他Polymer 2 Integrin alpha-5 × 1 （P08648） SG/19 Fab fragment (Light chain) × 1 SG/19 Fab fragment (Heavy chain) × 1 ;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 6 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 MAGNESIUM ION × 1 Consistent with protein count
2 Other combination Heteromer Protein 4 其他Polymer 2 Integrin alpha-5 × 1 （P08648） SG/19 Fab fragment (Light chain) × 1 SG/19 Fab fragment (Heavy chain) × 1 ;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CALCIUM ION × 6 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 MAGNESIUM ION × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
8rpq

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3g9w 3g9w 3t9k 3t9k 3vi3 3vi3 3vi4 3vi4 4dx9 4dx9 4dx9 4dx9

54 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name ITB1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–445； UniProt 21–465 Author chain D； PDBConstruct 1–445； UniProt 21–465

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_id3vi3
Deposition date deposition_date2011-09-21
Structure title titleCrystal structure of alpha5beta1 integrin headpiece (ligand-free form)
Keywords keywordsbeta propeller fold, Rossmann fold, beta sandwich, Fibronectin receptor, CELL ADHESION-IMMUNE SYSTEM complex; CELL ADHESION/IMMUNE SYSTEM
Experimental Method methodX-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.

3vi3__assembly_1__model_1

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

Download this curve (.dat)

3vi3__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3vi3__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）47.18 Å
Rg (electron density)47.51 Å
Total Rg47.61 Å
Atom count11437
Residues1465
Excluded volume202680 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3vi3__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3vi3__assembly_2__model_1 tetrameric （4） 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 (9)

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6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (10 domains)

Domain ID domain_idd3vi3a1
Class classb — All beta proteins
Fold Fold foldb.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamilyb.69.8 — Integrin alpha N-terminal domain
Family Family familyb.69.8.0 — automated matches
Domain ID domain_idd3vi3a2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.15 — Integrin domains
Family Family familyb.1.15.0 — automated matches
Domain ID domain_idd3vi3c1
Class classb — All beta proteins
Fold Fold foldb.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamilyb.69.8 — Integrin alpha N-terminal domain
Family Family familyb.69.8.0 — automated matches
Domain ID domain_idd3vi3c2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.15 — Integrin domains
Family Family familyb.1.15.0 — automated matches
Domain ID domain_idd3vi3e1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd3vi3e2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd3vi3f_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd3vi3h_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd3vi3l1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.0 — automated matches
Domain ID domain_idd3vi3l2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (18 domains)

Domain ID domain_id3vi3A01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily130 — Integrin alpha, N-terminal
Domain ID domain_id3vi3A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1460 — Integrin domains. Chain A, domain 2
Domain ID domain_id3vi3B01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1680 — ligand-binding face of the semaphorins, domain 2
Homologous superfamily homologous superfamily10 — ligand-binding face of the semaphorins, domain 2
Domain ID domain_id3vi3B02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1510 — ntegrin, alpha v. Chain A, domain 3
Domain ID domain_id3vi3B03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily410 — von Willebrand factor, type A domain
Domain ID domain_id3vi3C01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily130 — Integrin alpha, N-terminal
Domain ID domain_id3vi3C02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1460 — Integrin domains. Chain A, domain 2
Domain ID domain_id3vi3D01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1680 — ligand-binding face of the semaphorins, domain 2
Homologous superfamily homologous superfamily10 — ligand-binding face of the semaphorins, domain 2
Domain ID domain_id3vi3D02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1510 — ntegrin, alpha v. Chain A, domain 3
Domain ID domain_id3vi3D03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily410 — von Willebrand factor, type A domain
Domain ID domain_id3vi3E01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3vi3E02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3vi3F01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3vi3F02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3vi3H01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3vi3H02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3vi3L01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3vi3L02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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7. Citations (1)