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6vg4

Human protocadherin 10 ectodomain

Method: X-RAY DIFFRACTION Dmax: 231.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Protocadherin-10

Homo sapiens

UniProt Q9P2E7

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Monomer Protein × 1 其他Polymer 2 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 18–680 Not recorded 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 15 MAN alpha-D-mannopyranose × 3 TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 1 CL CHLORIDE ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；296 K；0.22M CaCl2, 0.1M Na Acetate pH 5.0 with 30% (v/v) glycerol as cryoprotectant and glutaraldehyde (0.5% v/v) added to the reservoir after crystal formation to aid crystal stability by cross-linking Resolution 3.30 Å R-free 0.284

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 6VG4 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6VFQ Crystal structure of monomeric human protocadherin 10 EC1-EC4 Deposited 2020-01-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 18–455（438 aa）
Not recorded CA CALCIUM ION × 9 MAN alpha-D-mannopyranose × 2 ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；296 K；14% PEG 400 (v/v), 0.1M sodium acetate pH 4.6, 0.1M CaCl2, with 30% ethylene glycol (v/v) added as cryoprotectant
Resolution 2.30 Å R-free 0.237
6VFW Crystal structure of human delta protocadherin 10 EC1-EC4 Deposited 2020-01-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 18–455（438 aa）
Chain C 18–455（438 aa）
Not recorded CA CALCIUM ION × 18 MAN alpha-D-mannopyranose × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；296 K；12% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 0.1M Tris-bicine buffer pH8.5, 10% 0.02 M D-glucose, 0.02 M D-mannose, 0.02 M D-galactose, 0.02 M L-fucose, 0.02 M D-xylose, 0.02 M N-acetyl-D-glucosamine with no further cryoprotection
Resolution 3.60 Å R-free 0.295
6VFW Crystal structure of human delta protocadherin 10 EC1-EC4 Deposited 2020-01-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 18–455（438 aa）
Chain D 18–455（438 aa）
Not recorded CA CALCIUM ION × 18 MAN alpha-D-mannopyranose × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；296 K；12% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 0.1M Tris-bicine buffer pH8.5, 10% 0.02 M D-glucose, 0.02 M D-mannose, 0.02 M D-galactose, 0.02 M L-fucose, 0.02 M D-xylose, 0.02 M N-acetyl-D-glucosamine with no further cryoprotection
Resolution 3.60 Å R-free 0.295
6VFW Crystal structure of human delta protocadherin 10 EC1-EC4 Deposited 2020-01-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 18–455（438 aa）
Not recorded CA CALCIUM ION × 18 MAN alpha-D-mannopyranose × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；296 K；12% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 0.1M Tris-bicine buffer pH8.5, 10% 0.02 M D-glucose, 0.02 M D-mannose, 0.02 M D-galactose, 0.02 M L-fucose, 0.02 M D-xylose, 0.02 M N-acetyl-D-glucosamine with no further cryoprotection
Resolution 3.60 Å R-free 0.295
9DQV Structure of western equine encephalitis virus CBA87 VLP in complex with human PCDH10 EC1 Deposited 2024-09-24 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 × 16 PDB declaration: 16-meric
Chain M 19–121（103 aa）
Chain N 19–121（103 aa）
Chain O 19–121（103 aa）
Chain P 19–121（103 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9E96 WEEV CBA87 VLP in complex with human PCDH10-EC1 Deposited 2024-11-07 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 × 16 PDB declaration: 16-meric
Chain H 19–122（104 aa）
Chain L 19–122（104 aa）
Chain P 19–122（104 aa）
Chain Q 19–122（104 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.05 Å
9L1N Structure of Western equine encephalitis virus 71V1658 strain VLP in complex with human PCDH10 EC1 Deposited 2024-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: 13-meric
Chain M 19–113（95 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9L41 Structure of WEEV strain 71V1658 virus-like particles (VLPs) in complex with human PCDH10 extracellular cadherin repeats 1-2 (EC1-EC2)(3-fold region) Deposited 2024-12-19 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 × 9 PDB declaration: nonameric
Chain R 19–114（96 aa）
Chain S 19–114（96 aa）
Chain T 19–114（96 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.99 Å

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PCD10_HUMAN
Isoform Q9P2E7-2
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–663； UniProt 18–680

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 6vg4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6vg4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6vg4
Deposition date deposition_date2020-01-07
Structure title titleHuman protocadherin 10 ectodomain
Keywords keywordscadherin, protocadherin, non-clustered, calcium binding, CELL ADHESION; CELL ADHESION
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_guinier79.96 Å
Radius of gyration Rg (electron density) rg_electron82.89 Å
Forward intensity I(0) i081096500.00
Molecular weight molecular_weight73306.0 kDa
Excluded volume excluded_volume90945 ų
Envelope volume envelope_volume177540 ų
Hydration-shell volume shell_volume22452 ų
Envelope diameter envelope_diameter274.6 Å
Shell Rg shell_rg51.06 Å
Envelope Rg envelope_rg81.56 Å
Shape Rg shape_rg82.91 Å
Total Rg total_rg81.97 Å
Total atoms total_atoms10078
Residues n_residues646
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 dmax231.8 Å
Rg (real space) rg_real78.70 Å
Rg uncertainty (real space) rg_real_error2.00 Å
I(0) (real space) i0_real8.0090e+07
I(0) uncertainty (real space) i0_real_error1.6720e+06
Rg (reciprocal space) rg_reciprocal73.34 Å
I(0) (reciprocal space) i0_reciprocal79680000.0000
Solution quality estimate total_estimate0.6073
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary23.2 Å
Skewness Skewness skewness0.445
Kurtosis Kurtosis kurtosis-0.915
Angular range angular_range— – 0.1000 Å−1
Current regularization parameter α current_alpha0.0164
Highest regularization parameter α highest_alpha4029000.0000
Real-space data points n_real_points21
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.016; Stabil: 0.936; Sysdev: 1.000; Positv: 1.000; Valcen: 0.050; Smooth: 0.872
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id6vg4A01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily60 — Cadherins
Domain ID domain_id6vg4A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily60 — Cadherins
Domain ID domain_id6vg4A03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily60 — Cadherins
Domain ID domain_id6vg4A04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily60 — Cadherins
Domain ID domain_id6vg4A05
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily60 — Cadherins
Domain ID domain_id6vg4A06
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily60 — Cadherins
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8. Citations (1)

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9. Files and Curves (10)