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4m8m

Crystal structure of the active dimer of zebrafish PlexinC1 cytoplasmic region

Method: X-RAY DIFFRACTION Dmax: 133.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

GCN4 coiled-coil fused zebrafish PlexinC1

Danio rerio

UniProt Q5RGW1

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 456–1056 Chain B； UniProt 456–1056 Fragment：zebrafish PlexinC1 cytoplasmic region, UNP residues 456-1056 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9.1；293 K；0.1M Bis-Tris propane, pH 9.1, 21% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 3.31 Å R-free 0.281

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 4M8M Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4M8N Crystal Structure of PlexinC1/Rap1B Complex Deposited 2013-08-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 455–1050（596 aa）
Chain D 455–1050（596 aa）
Not recorded MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 AF3 ALUMINUM FLUORIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；294.15 K；0.1 M HEPES, 5% 2-propanol, 25% PEG 3350, 3.6% polypropylene glycol P400, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 294.15K
Resolution 3.29 Å R-free 0.299
4M8N Crystal Structure of PlexinC1/Rap1B Complex Deposited 2013-08-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 455–1050（596 aa）
Chain C 455–1050（596 aa）
Not recorded MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 AF3 ALUMINUM FLUORIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；294.15 K；0.1 M HEPES, 5% 2-propanol, 25% PEG 3350, 3.6% polypropylene glycol P400, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 294.15K
Resolution 3.29 Å R-free 0.299

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q5RGW1_DANRE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 32–632； UniProt 456–1056 Author chain B； PDBConstruct 32–632； UniProt 456–1056

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 4m8m

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4m8m
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4m8m
Deposition date deposition_date2013-08-13
Structure title titleCrystal structure of the active dimer of zebrafish PlexinC1 cytoplasmic region
Keywords keywordsRasGAP-like fold, GAP for Rap GTPases, Rap, Membrane, SIGNALING PROTEIN; SIGNALING PROTEIN
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_guinier41.22 Å
Radius of gyration Rg (electron density) rg_electron40.89 Å
Forward intensity I(0) i0223630000.00
Molecular weight molecular_weight125730.0 kDa
Excluded volume excluded_volume158950 ų
Envelope volume envelope_volume220730 ų
Hydration-shell volume shell_volume47202 ų
Envelope diameter envelope_diameter142.6 Å
Shell Rg shell_rg43.89 Å
Envelope Rg envelope_rg40.90 Å
Shape Rg shape_rg40.89 Å
Total Rg total_rg41.08 Å
Total atoms total_atoms8871
Residues n_residues1147
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 dmax133.6 Å
Rg (real space) rg_real41.29 Å
Rg uncertainty (real space) rg_real_error1.17 Å
I(0) (real space) i0_real2.2360e+08
I(0) uncertainty (real space) i0_real_error3.9010e+06
Rg (reciprocal space) rg_reciprocal41.22 Å
I(0) (reciprocal space) i0_reciprocal223600000.0000
Solution quality estimate total_estimate0.8822
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary52.7 Å
Skewness Skewness skewness0.328
Kurtosis Kurtosis kurtosis-0.432
Angular range angular_range— – 0.1900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha38910000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.684
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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) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id4m8mA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology506 — GTPase Activation - p120GAP; domain 1
Homologous superfamily homologous superfamily10 — GTPase Activation - p120gap; domain 1
Domain ID domain_id4m8mA02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id4m8mB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology506 — GTPase Activation - p120GAP; domain 1
Homologous superfamily homologous superfamily10 — GTPase Activation - p120gap; domain 1
Domain ID domain_id4m8mB02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
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8. Citations (1)

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9. Files and Curves (10)