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5yxk

High resolution crystal structure of Human B7-2 IgV domain in P21 space group

Method: X-RAY DIFFRACTION Dmax: 94.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

T-lymphocyte activation antigen CD86

Homo sapiens

UniProt P42081

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 26–134 Chain B； UniProt 26–134 Fragment：Ig-like V-type No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.1M Tris HCl pH 8.5, 2.4M Ammonium phosphate dibasic Resolution 1.90 Å R-free 0.248
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 26–134 Chain D； UniProt 26–134 Fragment：Ig-like V-type No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.1M Tris HCl pH 8.5, 2.4M Ammonium phosphate dibasic Resolution 1.90 Å R-free 0.248

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5YXK Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1I85 CRYSTAL STRUCTURE OF THE CTLA-4/B7-2 COMPLEX Deposited 2001-03-12 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 26–134（109 aa） Fragment：IG V-TYPE (RECEPTOR BINDING) DOMAIN
Chain B 26–134（109 aa） Fragment：IG V-TYPE (RECEPTOR BINDING) DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；PEG20K, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.20 Å R-free 0.300
1NCN the receptor-binding domain of human B7-2 Deposited 2002-12-05 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–134（109 aa） Fragment：Ig V-type domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG4000, NaAC, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.70 Å R-free 0.278
1NCN the receptor-binding domain of human B7-2 Deposited 2002-12-05 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 26–134（109 aa） Fragment：Ig V-type domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG4000, NaAC, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.70 Å R-free 0.278
8FXX Cryo-EM structure of cowpox virus M2 in complex with human B7.2 (heptameric ring) Deposited 2023-01-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain C 26–134（109 aa）
Chain E 26–134（109 aa）
Chain G 26–134（109 aa）
Chain H 26–134（109 aa）
Chain J 26–134（109 aa）
Chain L 26–134（109 aa）
Chain N 26–134（109 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；150 mM Nacl, 25 mM HEPES, pH7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.26 Å
8FXY Cryo-EM structure of cowpox virus M2 in complex with human B7.2 (hexameric ring) Deposited 2023-01-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain C 26–243（218 aa）
Chain E 26–243（218 aa）
Chain G 26–243（218 aa）
Chain H 26–243（218 aa）
Chain J 26–243（218 aa）
Chain L 26–243（218 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；150 mM Nacl, 25 mM HEPES, pH7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.34 Å
8HXB Cryo-EM structure of MPXV M2 hexamer in complex with human B7.2 Deposited 2023-01-04 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain G 26–238（213 aa）
Chain H 26–238（213 aa）
Chain I 26–238（213 aa）
Chain J 26–238（213 aa）
Chain K 26–238（213 aa）
Chain L 26–238（213 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8HXC Cryo-EM structure of MPXV M2 heptamer in complex with human B7.2 Deposited 2023-01-04 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain H 26–238（213 aa）
Chain I 26–238（213 aa）
Chain J 26–238（213 aa）
Chain K 26–238（213 aa）
Chain L 26–238（213 aa）
Chain M 26–238（213 aa）
Chain N 26–238（213 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å

6 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CD86_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–111； UniProt 26–134 Author chain B； PDBConstruct 3–111； UniProt 26–134 Author chain C； PDBConstruct 3–111； UniProt 26–134 Author chain D； PDBConstruct 3–111； UniProt 26–134

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.

SAXS scattering curve SAXS Profile

SAXS profile for 5yxk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5yxk
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5yxk
Deposition date deposition_date2017-12-05
Structure title titleHigh resolution crystal structure of Human B7-2 IgV domain in P21 space group
Keywords keywordsB7-2, co-stimulatory molecule, Ig super family, CD86, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier27.54 Å
Radius of gyration Rg (electron density) rg_electron27.10 Å
Forward intensity I(0) i043778200.00
Molecular weight molecular_weight51256.0 kDa
Excluded volume excluded_volume64061 ų
Envelope volume envelope_volume80687 ų
Hydration-shell volume shell_volume26037 ų
Envelope diameter envelope_diameter97.2 Å
Shell Rg shell_rg32.59 Å
Envelope Rg envelope_rg27.19 Å
Shape Rg shape_rg27.07 Å
Total Rg total_rg27.77 Å
Total atoms total_atoms3603
Residues n_residues440
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax94.0 Å
Rg (real space) rg_real27.52 Å
Rg uncertainty (real space) rg_real_error0.86 Å
I(0) (real space) i0_real4.3780e+07
I(0) uncertainty (real space) i0_real_error6.7480e+05
Rg (reciprocal space) rg_reciprocal27.53 Å
I(0) (reciprocal space) i0_reciprocal43780000.0000
Solution quality estimate total_estimate0.8773
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.3 Å
Skewness Skewness skewness0.246
Kurtosis Kurtosis kurtosis-0.451
Angular range angular_range— – 0.2900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha19170000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.841; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.948; Smooth: 0.930
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd5yxka1
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_idd5yxka2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd5yxkb1
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_idd5yxkb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd5yxkc1
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_idd5yxkc2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd5yxkd1
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_idd5yxkd2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id5yxkA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5yxkB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5yxkC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5yxkD00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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8. Citations (1)

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9. Files and Curves (10)