← Back to search
1olz

The ligand-binding face of the semaphorins revealed by the high resolution crystal structure of SEMA4D

Method: X-RAY DIFFRACTION Dmax: 112.2 Å Quality: EXCELLENT
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

SEMAPHORIN 4D

Homo sapiens

UniProt Q92854

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 22–677 Chain B； UniProt 22–677 Fragment：SOLUBLE EXTRACELLULAR FRAGMENT, RESIDUES 22-677 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；0.2 M AMMONIUM FLORIDE, 20% PEG 3350, pH 7.50 Resolution 2.00 Å R-free 0.270

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 1OLZ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3OL2 Receptor-ligand structure of Human Semaphorin 4D with Plexin B1. Deposited 2010-08-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 22–677（656 aa） Fragment：Extracellular domains
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；294 K；0.1 M Tris,0.2 M calcium acetate, 6% v/v glycerol, 20% PEG3000, pH 7, VAPOR DIFFUSION, temperature 294K
Resolution 2.99 Å R-free 0.237

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

View Construct and Data Evidence
UniProt name SM4D_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–656； UniProt 22–677 Author chain B； PDBConstruct 1–656； UniProt 22–677

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 1olz

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1olz
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id1olz
Deposition date deposition_date2003-08-19
Structure title titleThe ligand-binding face of the semaphorins revealed by the high resolution crystal structure of SEMA4D
Keywords keywords;DEVELOPMENTAL PROTEIN, CD100, SEMAPHORIN, BETA-PROPELLER, PSI DOMAIN, IG-LIKE DOMAIN, EXTRACELLULAR RECEPTOR, NEUROGENESIS, GLYCOPROTEIN DEVELOPMENTAL PROTEIN, STRUCTURAL PROTEOMICS IN EUROPE, SPINE, STRUCTURAL GENOMICS ;; DEVELOPMENTAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier37.09 Å
Radius of gyration Rg (electron density) rg_electron36.20 Å
Forward intensity I(0) i0293138000.00
Molecular weight molecular_weight139440.0 kDa
Excluded volume excluded_volume174850 ų
Envelope volume envelope_volume230060 ų
Hydration-shell volume shell_volume51979 ų
Envelope diameter envelope_diameter115.4 Å
Shell Rg shell_rg43.59 Å
Envelope Rg envelope_rg35.44 Å
Shape Rg shape_rg36.19 Å
Total Rg total_rg36.73 Å
Total atoms total_atoms9828
Residues n_residues1244
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
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax112.2 Å
Rg (real space) rg_real36.88 Å
Rg uncertainty (real space) rg_real_error0.63 Å
I(0) (real space) i0_real2.9310e+08
I(0) uncertainty (real space) i0_real_error4.1560e+06
Rg (reciprocal space) rg_reciprocal37.02 Å
I(0) (reciprocal space) i0_reciprocal293200000.0000
Solution quality estimate total_estimate0.9099
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary49.6 Å
Skewness Skewness skewness0.048
Kurtosis Kurtosis kurtosis-0.680
Angular range angular_range— – 0.2150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha29230000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.974; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.907
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1olza1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.4 — I set domains
Domain ID domain_idd1olza2
Class classb — All beta proteins
Fold Fold foldb.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamilyb.69.12 — Sema domain
Family Family familyb.69.12.1 — Sema domain
Domain ID domain_idd1olza3
Class classg — Small proteins
Fold Fold foldg.16 — Trefoil/Plexin domain-like
Superfamily Superfamily superfamilyg.16.2 — Plexin repeat
Family Family familyg.16.2.1 — Plexin repeat
Domain ID domain_idd1olzb1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.4 — I set domains
Domain ID domain_idd1olzb2
Class classb — All beta proteins
Fold Fold foldb.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamilyb.69.12 — Sema domain
Family Family familyb.69.12.1 — Sema domain
Domain ID domain_idd1olzb3
Class classg — Small proteins
Fold Fold foldg.16 — Trefoil/Plexin domain-like
Superfamily Superfamily superfamilyg.16.2 — Plexin repeat
Family Family familyg.16.2.1 — Plexin repeat

CATH v4.4 (6 domains)

Domain ID domain_id1olzA01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id1olzA02
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_id1olzA03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1olzB01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id1olzB02
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_id1olzB03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
▶

8. Citations (1)

▶

9. Files and Curves (10)