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3p8c

Structure and Control of the Actin Regulatory WAVE Complex

Method: X-RAY DIFFRACTION Dmax: 188.6 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cytoplasmic FMR1-interacting protein 1

Homo sapiens

UniProt Q7L576

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 heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count Chain A； UniProt 1–1253 Not recorded Nck-associated protein 1 × 1 （Q9Y2A7） Wiskott-Aldrich syndrome protein family member 1 × 1 （Q92558） Probable protein BRICK1 × 1 （Q8WUW1） Abl interactor 2 × 1 （B4DSN1） TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 CL CHLORIDE ION × 7 GOL GLYCEROL × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；10 % (w/v) glycerol, 4 % PEG 10,000, 12-20 % PEG 300, 100 mM Tris-HCl, 2 mM TCEP, 2 mM EDTA, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.29 Å R-free 0.237

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 3P8C Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4N78 The WAVE Regulatory Complex Links Diverse Receptors to the Actin Cytoskeleton Deposited 2013-10-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–1253（1253 aa）
Not recorded CL CHLORIDE ION × 4 GOL GLYCEROL × 16 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8.5；277 K；10% glycerol, 4% PEG 10,000, 12-20% PEG 300, 100 mM Tris-HCl, 2mM EDTA, 2 mM TCEP, pH 8.5, EVAPORATION, temperature 277K
Resolution 2.43 Å R-free 0.209
7USC Cryo-EM structure of WAVE Regulatory Complex Deposited 2022-04-25 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–1253（1253 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7USD Cryo-EM structure of D-site Rac1-bound WAVE Regulatory Complex Deposited 2022-04-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–1253（1253 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7USE Cryo-EM structure of WAVE regulatory complex with Rac1 bound on both A and D site Deposited 2022-04-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 1–1253（1253 aa）
Not recorded GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CYFP1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–1253； UniProt 1–1253

Nck-associated protein 1

Homo sapiens

UniProt Q9Y2A7

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 heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count Chain B； UniProt 1–1128 Not recorded Cytoplasmic FMR1-interacting protein 1 × 1 （Q7L576） Wiskott-Aldrich syndrome protein family member 1 × 1 （Q92558） Probable protein BRICK1 × 1 （Q8WUW1） Abl interactor 2 × 1 （B4DSN1） TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 CL CHLORIDE ION × 7 GOL GLYCEROL × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；10 % (w/v) glycerol, 4 % PEG 10,000, 12-20 % PEG 300, 100 mM Tris-HCl, 2 mM TCEP, 2 mM EDTA, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.29 Å R-free 0.237

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 3P8C Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4N78 The WAVE Regulatory Complex Links Diverse Receptors to the Actin Cytoskeleton Deposited 2013-10-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 1–1128（1128 aa）
Not recorded CL CHLORIDE ION × 4 GOL GLYCEROL × 16 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8.5；277 K；10% glycerol, 4% PEG 10,000, 12-20% PEG 300, 100 mM Tris-HCl, 2mM EDTA, 2 mM TCEP, pH 8.5, EVAPORATION, temperature 277K
Resolution 2.43 Å R-free 0.209
7USC Cryo-EM structure of WAVE Regulatory Complex Deposited 2022-04-25 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 1–1128（1128 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7USD Cryo-EM structure of D-site Rac1-bound WAVE Regulatory Complex Deposited 2022-04-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 1–1128（1128 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7USE Cryo-EM structure of WAVE regulatory complex with Rac1 bound on both A and D site Deposited 2022-04-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain B 1–1128（1128 aa）
Not recorded GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NCKP1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–1128； UniProt 1–1128

Wiskott-Aldrich syndrome protein family member 1

Homo sapiens

UniProt Q92558

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 heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count Chain D； UniProt 1–186 Chain D； UniProt 485–559 Mutation：prolin rich region deletion mutant Cytoplasmic FMR1-interacting protein 1 × 1 （Q7L576） Nck-associated protein 1 × 1 （Q9Y2A7） Probable protein BRICK1 × 1 （Q8WUW1） Abl interactor 2 × 1 （B4DSN1） TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 CL CHLORIDE ION × 7 GOL GLYCEROL × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；10 % (w/v) glycerol, 4 % PEG 10,000, 12-20 % PEG 300, 100 mM Tris-HCl, 2 mM TCEP, 2 mM EDTA, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.29 Å R-free 0.237

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 3P8C Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4N78 The WAVE Regulatory Complex Links Diverse Receptors to the Actin Cytoskeleton Deposited 2013-10-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain D 1–559（559 aa）
Not recorded CL CHLORIDE ION × 4 GOL GLYCEROL × 16 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8.5；277 K；10% glycerol, 4% PEG 10,000, 12-20% PEG 300, 100 mM Tris-HCl, 2mM EDTA, 2 mM TCEP, pH 8.5, EVAPORATION, temperature 277K
Resolution 2.43 Å R-free 0.209
7USC Cryo-EM structure of WAVE Regulatory Complex Deposited 2022-04-25 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–230（230 aa）
Chain C 485–559（75 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7USD Cryo-EM structure of D-site Rac1-bound WAVE Regulatory Complex Deposited 2022-04-25 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 × 6 PDB declaration: hexameric
Chain C 1–230（230 aa）
Chain C 485–559（75 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7USE Cryo-EM structure of WAVE regulatory complex with Rac1 bound on both A and D site Deposited 2022-04-25 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 × 7 PDB declaration: heptameric
Chain C 1–230（230 aa）
Chain C 485–559（75 aa）
Not recorded GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name WASF1_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain D； PDBConstruct 1–186； UniProt 1–186 Author chain D； PDBConstruct 205–279； UniProt 485–559

Probable protein BRICK1

Homo sapiens

UniProt Q8WUW1

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 heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count Chain E； UniProt 1–75 Not recorded Cytoplasmic FMR1-interacting protein 1 × 1 （Q7L576） Nck-associated protein 1 × 1 （Q9Y2A7） Wiskott-Aldrich syndrome protein family member 1 × 1 （Q92558） Abl interactor 2 × 1 （B4DSN1） TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 CL CHLORIDE ION × 7 GOL GLYCEROL × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；10 % (w/v) glycerol, 4 % PEG 10,000, 12-20 % PEG 300, 100 mM Tris-HCl, 2 mM TCEP, 2 mM EDTA, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.29 Å R-free 0.237

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 3P8C Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4N78 The WAVE Regulatory Complex Links Diverse Receptors to the Actin Cytoskeleton Deposited 2013-10-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 1–75（75 aa）
Not recorded CL CHLORIDE ION × 4 GOL GLYCEROL × 16 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8.5；277 K；10% glycerol, 4% PEG 10,000, 12-20% PEG 300, 100 mM Tris-HCl, 2mM EDTA, 2 mM TCEP, pH 8.5, EVAPORATION, temperature 277K
Resolution 2.43 Å R-free 0.209
7USC Cryo-EM structure of WAVE Regulatory Complex Deposited 2022-04-25 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 1–75（75 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7USD Cryo-EM structure of D-site Rac1-bound WAVE Regulatory Complex Deposited 2022-04-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain D 1–75（75 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7USE Cryo-EM structure of WAVE regulatory complex with Rac1 bound on both A and D site Deposited 2022-04-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain D 1–75（75 aa）
Not recorded GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BRK1_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain E； PDBConstruct 1–75； UniProt 1–75

Abl interactor 2

Homo sapiens

UniProt B4DSN1

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 heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count Chain F； UniProt 1–158 Fragment：N-terminal domain Cytoplasmic FMR1-interacting protein 1 × 1 （Q7L576） Nck-associated protein 1 × 1 （Q9Y2A7） Wiskott-Aldrich syndrome protein family member 1 × 1 （Q92558） Probable protein BRICK1 × 1 （Q8WUW1） TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 CL CHLORIDE ION × 7 GOL GLYCEROL × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；10 % (w/v) glycerol, 4 % PEG 10,000, 12-20 % PEG 300, 100 mM Tris-HCl, 2 mM TCEP, 2 mM EDTA, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.29 Å R-free 0.237

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name B4DSN1_HUMAN
Isoform —
PDB entities 5
Chains and sequence ranges Author chain F； PDBConstruct 2–159； UniProt 1–158

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 3p8c

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3p8c
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3p8c
Deposition date deposition_date2010-10-13
Structure title titleStructure and Control of the Actin Regulatory WAVE Complex
Keywords keywordsactin polymerization, PROTEIN BINDING; PROTEIN BINDING
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_guinier58.52 Å
Radius of gyration Rg (electron density) rg_electron59.47 Å
Forward intensity I(0) i01350630000.00
Molecular weight molecular_weight311020.0 kDa
Excluded volume excluded_volume391260 ų
Envelope volume envelope_volume553130 ų
Hydration-shell volume shell_volume84675 ų
Envelope diameter envelope_diameter209.9 Å
Shell Rg shell_rg52.32 Å
Envelope Rg envelope_rg59.58 Å
Shape Rg shape_rg59.47 Å
Total Rg total_rg59.26 Å
Total atoms total_atoms21828
Residues n_residues2685
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 dmax188.6 Å
Rg (real space) rg_real59.34 Å
Rg uncertainty (real space) rg_real_error1.80 Å
I(0) (real space) i0_real1.3510e+09
I(0) uncertainty (real space) i0_real_error2.7110e+07
Rg (reciprocal space) rg_reciprocal57.79 Å
I(0) (reciprocal space) i0_reciprocal1347000000.0000
Solution quality estimate total_estimate0.5444
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary48.9 Å
Skewness Skewness skewness0.634
Kurtosis Kurtosis kurtosis-0.319
Angular range angular_range— – 0.1350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha199200000.0000
Real-space data points n_real_points28
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.735; Stabil: 1.000; Sysdev: 0.009; Positv: 1.000; Valcen: 0.805; Smooth: 0.034
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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) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id3p8cD01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily340 —
Domain ID domain_id3p8cD02
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology280 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily150 —
Domain ID domain_id3p8cE01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily110 —
Domain ID domain_id3p8cF01
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily1620 —
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8. Citations (1)

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9. Files and Curves (10)