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2bnx

Crystal structure of the dimeric regulatory domain of mouse diaphaneous-related formin (DRF), mDia1

Method: X-RAY DIFFRACTION Dmax: 106.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DIAPHANOUS PROTEIN HOMOLOG 1

MUS MUSCULUS

UniProt O08808

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 131–516 Chain B； UniProt 131–516 Fragment：AMINO-TERMINAL DOMAIN, RESIDUES 131-516 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.25；HANGING DROP VAPOR DIFFUSION; PROTEIN: 11 MG/ML IN 100 MM HEPES, PH 7.25; RESERVOIR: 100 MM HEPES, PH 7.25, 9% PEG3350 Resolution 2.40 Å R-free 0.236

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 2BNX Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1V9D Crystal structure of the core FH2 domain of mouse mDia1 Deposited 2004-01-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 826–1163（338 aa） Fragment：core FH2 domain
Chain B 826–1163（338 aa） Fragment：core FH2 domain
Chain C 826–1163（338 aa） Fragment：core FH2 domain
Chain D 826–1163（338 aa） Fragment：core FH2 domain
Not recorded SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；293 K；PEG3350, sodium sulfate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.60 Å R-free 0.267
1Z2C Crystal structure of mDIA1 GBD-FH3 in complex with RhoC-GMPPNP Deposited 2005-03-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 69–451（383 aa）
Not recorded MG MAGNESIUM ION × 4 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；PEG 2000-MME, magnesium sulphate, Tris buffer, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.00 Å R-free 0.285
1Z2C Crystal structure of mDIA1 GBD-FH3 in complex with RhoC-GMPPNP Deposited 2005-03-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 69–451（383 aa）
Not recorded MG MAGNESIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；PEG 2000-MME, magnesium sulphate, Tris buffer, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.00 Å R-free 0.285
2BAP Crystal structure of the N-terminal mDia1 Armadillo Repeat Region and Dimerisation Domain in complex with the mDia1 autoregulatory domain (DAD) Deposited 2005-10-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 135–451（317 aa） Fragment：mDia1 N-terminal regulatory domain
Chain C 1145–1200（56 aa） Fragment：mDia1 autoregulatory domain, DAD
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；293 K；3.7 M NaFormiate pH 7.1, 100 mM HEPES pH 7.1, 4% (w/v) PEG5000-MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.30 Å R-free 0.364
2BAP Crystal structure of the N-terminal mDia1 Armadillo Repeat Region and Dimerisation Domain in complex with the mDia1 autoregulatory domain (DAD) Deposited 2005-10-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain B 135–451（317 aa） Fragment：mDia1 N-terminal regulatory domain
Chain D 1145–1200（56 aa） Fragment：mDia1 autoregulatory domain, DAD
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；293 K；3.7 M NaFormiate pH 7.1, 100 mM HEPES pH 7.1, 4% (w/v) PEG5000-MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.30 Å R-free 0.364
2F31 Crystal structure of the autoinhibitory switch in Formin mDia1; the DID/DAD complex Deposited 2005-11-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 135–367（233 aa）
Chain B 1177–1196（20 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M sodium citrate, 200 mM ammonium sulfate, 25% PEG 4000, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.10 Å R-free 0.312
2F31 Crystal structure of the autoinhibitory switch in Formin mDia1; the DID/DAD complex Deposited 2005-11-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 135–367（233 aa）
Chain B 1177–1196（20 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M sodium citrate, 200 mM ammonium sulfate, 25% PEG 4000, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.10 Å R-free 0.312
2V8F Mouse Profilin IIa in complex with a double repeat from the FH1 domain of mDia1 Deposited 2007-08-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 635–655（21 aa） Fragment：FH1 DOMAIN, RESIDUES 635-655
Not recorded SO4 SULFATE ION × 5 NA SODIUM ION × 1 GOL GLYCEROL × 1 IPA ISOPROPYL ALCOHOL × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.10 Å R-free 0.173
3EG5 Crystal structure of MDIA1-TSH GBD-FH3 in complex with CDC42-GMPPNP Deposited 2008-09-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 69–451（383 aa） Fragment：MDIAN-TSH, UNP residues 69-451
Chain D 69–451（383 aa） Fragment：MDIAN-TSH, UNP residues 69-451
Mutation：N164T, N165S, N166H Mutation：N164T, N165S, N166H GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；293 K；Bis-Tris-Propane (PH 8.8 adjusted with citric acid), 26% (w/v) PEG 3350, 250mM Na-Tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.70 Å R-free 0.243
3O4X Crystal structure of complex between amino and carboxy terminal fragments of mDia1 Deposited 2010-07-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 131–458（328 aa） Fragment：mDia1 N-terminal regulatory domain (unp residues 131-458)
Chain D 131–458（328 aa） Fragment：mDia1 N-terminal regulatory domain (unp residues 131-458)
Chain E 736–1200（465 aa） Fragment：mDia1 C-terminal FH2-DAD domain (unp residues 736-1200)
Chain H 736–1200（465 aa） Fragment：mDia1 C-terminal FH2-DAD domain (unp residues 736-1200)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；313 K；Peg 4000, sodium malonate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 313K
Resolution 3.20 Å R-free 0.298
3O4X Crystal structure of complex between amino and carboxy terminal fragments of mDia1 Deposited 2010-07-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain B 131–458（328 aa） Fragment：mDia1 N-terminal regulatory domain (unp residues 131-458)
Chain C 131–458（328 aa） Fragment：mDia1 N-terminal regulatory domain (unp residues 131-458)
Chain F 736–1200（465 aa） Fragment：mDia1 C-terminal FH2-DAD domain (unp residues 736-1200)
Chain G 736–1200（465 aa） Fragment：mDia1 C-terminal FH2-DAD domain (unp residues 736-1200)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；313 K；Peg 4000, sodium malonate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 313K
Resolution 3.20 Å R-free 0.298
3OBV Autoinhibited Formin mDia1 Structure Deposited 2010-08-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: dimeric
Chain A 131–457（327 aa） Fragment：N-terminal fragment, UNP residues 131-457
Chain B 131–457（327 aa） Fragment：N-terminal fragment, UNP residues 131-457
Chain E 753–1209（457 aa） Fragment：C-terminal fragment, UNP residues 753-1209
Chain F 753–1209（457 aa） Fragment：C-terminal fragment, UNP residues 753-1209
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.75；293 K；10% PEG 1500, 25% sucrose, 0.1 M MES pH 6.75, 0.15 M NaCl, 1 mM DTT, vapor diffusion, hanging drop, temperature 293K
Resolution 2.75 Å R-free 0.261
3OBV Autoinhibited Formin mDia1 Structure Deposited 2010-08-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Homooligomer；Protein × 4 PDB declaration: dimeric
Chain C 131–457（327 aa） Fragment：N-terminal fragment, UNP residues 131-457
Chain D 131–457（327 aa） Fragment：N-terminal fragment, UNP residues 131-457
Chain G 753–1209（457 aa） Fragment：C-terminal fragment, UNP residues 753-1209
Chain H 753–1209（457 aa） Fragment：C-terminal fragment, UNP residues 753-1209
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.75；293 K；10% PEG 1500, 25% sucrose, 0.1 M MES pH 6.75, 0.15 M NaCl, 1 mM DTT, vapor diffusion, hanging drop, temperature 293K
Resolution 2.75 Å R-free 0.261
4UWX Structure of liprin-alpha3 in complex with mDia1 Diaphanous- inhibitory domain Deposited 2014-08-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 135–369（235 aa） Fragment：DIAPHANOUS-INHIBITORY DOMAIN, RESIDUES 135-369
Not recorded NI NICKEL (II) ION × 1 144 TRIS-HYDROXYMETHYL-METHYL-AMMONIUM × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；0.2 M NACL, 0.1 M TRIS/HCL PH 8.0, 20% PEG6000
Resolution 1.65 Å R-free 0.210
4UWX Structure of liprin-alpha3 in complex with mDia1 Diaphanous- inhibitory domain Deposited 2014-08-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 135–369（235 aa） Fragment：DIAPHANOUS-INHIBITORY DOMAIN, RESIDUES 135-369
Not recorded NI NICKEL (II) ION × 1 144 TRIS-HYDROXYMETHYL-METHYL-AMMONIUM × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；0.2 M NACL, 0.1 M TRIS/HCL PH 8.0, 20% PEG6000
Resolution 1.65 Å R-free 0.210
8RU2 Structure of the F-actin barbed end bound by formin mDia1 Deposited 2024-01-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 552–584（33 aa）
Chain E 721–1255（535 aa）
Chain F 552–584（33 aa）
Chain F 721–1255（535 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.1
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；3 seconds, force 0.
Resolution 3.49 Å
9B27 Dia1 at the Barbed End of F-Actin Deposited 2024-03-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain G 745–1166（422 aa）
Chain H 745–1166（422 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 MG MAGNESIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.51 Å
9B3D mDia1 in the middle of F-actin Deposited 2024-03-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain G 745–1143（399 aa）
Chain H 745–1143（399 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 6 MG MAGNESIUM ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20mM HEPES, 50mM NaCL, 1mM EDTA, 1mM DTT, 0.05% Thesit
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.41 Å

12 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DIAP1_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–386； UniProt 131–516 Author chain B； PDBConstruct 1–386； UniProt 131–516

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 2bnx

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2bnx
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2bnx
Deposition date deposition_date2005-04-05
Structure title titleCrystal structure of the dimeric regulatory domain of mouse diaphaneous-related formin (DRF), mDia1
Keywords keywordsAUTOINHIBITION, ACTIN, NUCLEATION, CYTOSKELETON, STRUCTURAL PROTEIN; STRUCTURAL 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_guinier33.44 Å
Radius of gyration Rg (electron density) rg_electron32.76 Å
Forward intensity I(0) i097568300.00
Molecular weight molecular_weight77297.0 kDa
Excluded volume excluded_volume96391 ų
Envelope volume envelope_volume129200 ų
Hydration-shell volume shell_volume33847 ų
Envelope diameter envelope_diameter113.0 Å
Shell Rg shell_rg38.21 Å
Envelope Rg envelope_rg32.56 Å
Shape Rg shape_rg32.74 Å
Total Rg total_rg33.26 Å
Total atoms total_atoms5404
Residues n_residues677
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 dmax106.9 Å
Rg (real space) rg_real33.47 Å
Rg uncertainty (real space) rg_real_error0.87 Å
I(0) (real space) i0_real9.7570e+07
I(0) uncertainty (real space) i0_real_error1.5040e+06
Rg (reciprocal space) rg_reciprocal33.45 Å
I(0) (reciprocal space) i0_reciprocal97570000.0000
Solution quality estimate total_estimate0.8944
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary31.8 Å
Skewness Skewness skewness0.261
Kurtosis Kurtosis kurtosis-0.658
Angular range angular_range— – 0.2350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha21050000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.915; Smooth: 0.893
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2bnxa1
Class classa — All alpha proteins
Fold Fold folda.118 — alpha-alpha superhelix
Superfamily Superfamily superfamilya.118.1 — ARM repeat
Family Family familya.118.1.23 — Diap1 N-terninal region-like
Domain ID domain_idd2bnxb_
Class classa — All alpha proteins
Fold Fold folda.118 — alpha-alpha superhelix
Superfamily Superfamily superfamilya.118.1 — ARM repeat
Family Family familya.118.1.23 — Diap1 N-terninal region-like

CATH v4.4 (4 domains)

Domain ID domain_id2bnxA01
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily10 — Leucine-rich Repeat Variant
Domain ID domain_id2bnxA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily150 — Formin, FH3 diaphanous domain
Domain ID domain_id2bnxB01
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily10 — Leucine-rich Repeat Variant
Domain ID domain_id2bnxB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily150 — Formin, FH3 diaphanous domain
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8. Citations (1)

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9. Files and Curves (10)