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6vfw

Crystal structure of human delta protocadherin 10 EC1-EC4

Method: X-RAY DIFFRACTION Dmax: 230.3 Å Quality: SUSPICIOUS
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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 Homooligomer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 18–455 Chain C； UniProt 18–455 Not recorded ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 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
2 Other combination Homooligomer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 18–455 Chain D； UniProt 18–455 Not recorded ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 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
3 Other combination Homooligomer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain E； UniProt 18–455 Not recorded ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 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

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 6VFW 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 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
6VG4 Human protocadherin 10 ectodomain Deposited 2020-01-07 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 18–680（663 aa）
Not recorded 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
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 6 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 1–438； UniProt 18–455 Author chain B； PDBConstruct 1–438； UniProt 18–455 Author chain C； PDBConstruct 1–438； UniProt 18–455 Author chain D； PDBConstruct 1–438； UniProt 18–455 Author chain E； PDBConstruct 1–438； UniProt 18–455

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 6vfw

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6vfw
Deposition date deposition_date2020-01-06
Structure title titleCrystal structure of human delta protocadherin 10 EC1-EC4
Keywords keywords;cadherin extracellular region, non-clustered delta2 family, protocadherin, homophilic adhesion/recognition calcium-dependent, adhesion molecule, 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_guinier68.47 Å
Radius of gyration Rg (electron density) rg_electron70.59 Å
Forward intensity I(0) i0876952000.00
Molecular weight molecular_weight240940.0 kDa
Excluded volume excluded_volume299080 ų
Envelope volume envelope_volume481320 ų
Hydration-shell volume shell_volume72182 ų
Envelope diameter envelope_diameter304.1 Å
Shell Rg shell_rg50.02 Å
Envelope Rg envelope_rg71.08 Å
Shape Rg shape_rg70.64 Å
Total Rg total_rg69.81 Å
Total atoms total_atoms32966
Residues n_residues2120
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 dmax230.3 Å
Rg (real space) rg_real67.61 Å
Rg uncertainty (real space) rg_real_error2.26 Å
I(0) (real space) i0_real8.7100e+08
I(0) uncertainty (real space) i0_real_error1.8400e+07
Rg (reciprocal space) rg_reciprocal64.80 Å
I(0) (reciprocal space) i0_reciprocal869600000.0000
Solution quality estimate total_estimate0.4887
Solution quality rating solution_quality SUSPICIOUS a SUSPICIOUS solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary50.1 Å
Skewness Skewness skewness0.755
Kurtosis Kurtosis kurtosis-0.092
Angular range angular_range— – 0.1150 Å−1
Current regularization parameter α current_alpha0.0117
Highest regularization parameter α highest_alpha98420000.0000
Real-space data points n_real_points24
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.001; Oscil: 0.447; Stabil: 0.995; Sysdev: 0.038; Positv: 1.000; Valcen: 0.463; Smooth: 0.428
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 15 domains

CATH v4.4 (15 domains)

Domain ID domain_id6vfwA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily60 — Cadherins
Domain ID domain_id6vfwA03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily60 — Cadherins
Domain ID domain_id6vfwA04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily60 — Cadherins
Domain ID domain_id6vfwB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily60 — Cadherins
Domain ID domain_id6vfwB03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily60 — Cadherins
Domain ID domain_id6vfwB04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily60 — Cadherins
Domain ID domain_id6vfwC02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily60 — Cadherins
Domain ID domain_id6vfwC03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily60 — Cadherins
Domain ID domain_id6vfwC04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily60 — Cadherins
Domain ID domain_id6vfwD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily60 — Cadherins
Domain ID domain_id6vfwD03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily60 — Cadherins
Domain ID domain_id6vfwD04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily60 — Cadherins
Domain ID domain_id6vfwE02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily60 — Cadherins
Domain ID domain_id6vfwE03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily60 — Cadherins
Domain ID domain_id6vfwE04
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)