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Crystal structure of racemic villin headpiece subdomain in space group I-4c2

Method: X-RAY DIFFRACTION D_max: 35.1 Å Quality: GOOD

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

D-Villin-1

OrganismNot specified

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 792–826	Fragment：headpiece subdomain (UNP residues 792-826) Mutation：N818H Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.75；298 K；2.0 M ammonium sulfate, 6% isopropanol, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.230

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 3TRY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1QQV SOLUTION STRUCTURE OF THE HEADPIECE DOMAIN OF CHICKEN VILLIN Deposited 1999-06-08	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 760–826（67 aa） Fragment：HP67	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；293 K；Ionic strength (raw mmCIF value) LOW；Pressure AMBIENT NMR measurement conditions pH 7；293 K；Ionic strength (raw mmCIF value) LOW；Pressure AMBIENT NMR measurement conditions pH 7；293 K；Ionic strength (raw mmCIF value) LOW；Pressure AMBIENT NMR measurement conditions pH 7；293 K；Ionic strength (raw mmCIF value) LOW；Pressure AMBIENT NMR sample composition 1 MM HP67, 10 MM PHOSPHATE BUFFER, PH 7.0 NMR sample composition 1 MM HP67 U-15N , 10 MM PHOSPHATE BUFFER, PH 7.0 NMR sample composition 1 MM HP67 U-15N,10% 13C, 10 MM PHOSPHATE BUFFER, PH 7.0 NMR sample composition 1 MM HP67	Resolution not provided
1VII THERMOSTABLE SUBDOMAIN FROM CHICKEN VILLIN HEADPIECE, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1997-01-15	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 792–826（35 aa） Fragment：THERMOSTABLE SUBDOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 3.7；303 K	Resolution not provided
1WY3 Chicken villin subdomain HP-35, K65(NLE), N68H, pH7.0 Deposited 2005-02-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 792–826（35 aa） Fragment：VHP	Mutation：K65(NLE), N68H Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；293 K；1ul 50mg/ml peptide plus 1ul (200mM KFormate, 20% PEG3350), pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 7.00	Resolution 0.95 Å R-free 0.171
1WY4 Chicken villin subdomain HP-35, K65(NLE), N68H, pH5.1 Deposited 2005-02-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 792–826（35 aa） Fragment：VHP	Mutation：K65(NLE), N68H Non-standard monomer：Yes (specific site not provided by mmCIF)	IOD IODIDE ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.1；293 K；1ul 50mg/ml peptide plus 1ul (200mM AmCitrate, 20% PEF3350), pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 5.10	Resolution 1.55 Å R-free 0.213
1YRF Chicken villin subdomain HP-35, N68H, pH6.7 Deposited 2005-02-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 792–826（35 aa） Fragment：VHP	Mutation：N68H	SO4 SULFATE ION × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.7；293 K；1ul 100mg/ml peptide plus 1ul (200mM NaOAc, 2.2M AmSO4), pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 6.70	Resolution 1.07 Å R-free 0.161
1YRI Chicken villin subdomain HP-35, N68H, pH6.4 Deposited 2005-02-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 792–826（35 aa） Fragment：VHP	Mutation：N68H	ACT ACETATE ION × 1 IOD IODIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.4；293 K；1ul 100mg/ml peptide plus 1ul (200mM AmOAc, 100mM NaCitrate, 30% PEG4000), pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 6.40	Resolution 1.00 Å R-free 0.205
1YU5 Crystal Structure of the Headpiece Domain of Chicken Villin Deposited 2005-02-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 760–826（67 aa） Fragment：Headpiece	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；1.5 M Na,K Phosphate buffer, 100 mM 2-(4-(2-Hydroxyethyl)-1-piperzainyl) ethanesulfonic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.40 Å R-free 0.216
1YU7 Crystal Structure of the W64Y mutant of Villin Headpiece Deposited 2005-02-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 760–826（67 aa） Fragment：Residue 10-76	Mutation：W64Y	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.2 M ammonium Sulfate, 0.1 M sodium cacodylate (pH 6.5) and 30 % polyethylene glycol (PEG) 8,000, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.50 Å R-free 0.210
1YU8 Crystal Structure of the R37A Mutant of Villin Headpiece Deposited 2005-02-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 760–826（67 aa） Fragment：Residue 10-76	Mutation：R37A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.2 M ammonium Sulfate, 0.1 M sodium cacodylate (pH 6.5) and 30 % polyethylene glycol (PEG) 8,000, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.45 Å R-free 0.211
2F4K Chicken villin subdomain HP-35, K65(NLE), N68H, K70(NLE), PH9 Deposited 2005-11-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 792–826（35 aa） Fragment：residues 792-826	Mutation：N68H Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions Initial drop contained 1ul 90mg/ml protein in 10mM Tris (pH7.4) and 7.5% v/v trifluoroethanol (TFE) and 1ul reservoir solution. Precipitant in reservoir was (initial: 800mM AmSO4, 100mM Bicine (pH 9.0), 10% v/v TFE) and (final: 1.6M AmSO4, 100mM Bicine (pH 9.0), 7.5% v/v TFE). Reservoir solution was changed from initial to final after one week.	Resolution 1.05 Å R-free 0.166
2JM0 Solution structure of chicken villin headpiece subdomain containing a fluorinated side chain in the core Deposited 2006-09-06	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 792–826（35 aa） Fragment：residues 792-826	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；298 K；Ionic strength (raw mmCIF value) 10；Pressure ambient NMR sample composition 4 mM F5-Phe-cVHP \| 93% H2O/7% D2O NMR sample composition 2 mM selectively 15N-[Ala, Phe, Leu] F5-Phe-cVHP \| 93% H2O/7% D2O	Resolution not provided
2LLF Sixth Gelsolin-like domain of villin in 5 mM CaCl2 Deposited 2011-11-07	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 619–725（107 aa） Fragment：Gelsolin-like 6 domain containing residues 619-725	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Pressure ambient NMR sample composition 50 M H2O, 5 M [U-2H] D2O, 10 mM [U-2H] DTT, 0.01 % sodium azide, 5 mM Calcium Chloride, 20 mM [U-2H] PIPES, 1 mM [U-99% 13C; U-99% 15N] D6, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 50 M H2O, 5 M [U-2H] D2O, 10 mM [U-2H] DTT, 0.01 % sodium azide, 5 mM Calcium Chloride, 20 mM [U-2H] PIPES, 1 mM D6, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 55 M [U-2H] D2O, 10 mM [U-2H] DTT, 0.01 % sodium azide, 5 mM Calcium Chloride, 20 mM [U-2H] PIPES, 1 mM D6, 100% D2O \| 100% D2O	Resolution not provided
2PPZ NMR solution Structure of the Villin Headpiece Mutant G34L Deposited 2007-05-01	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 792–826（35 aa） Fragment：C-terminal residues of headpiece domain, sequence database residues 792-826	Mutation：G34L	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；298 K；Pressure ambient NMR sample composition 4.3 mg peptide dissolved in 0.5 ml 90% H2O, 10% D2O (v/v) and 0.1 mM 2,2-dimethyl-2-silapentane sulfonic acid (DSS) for internal referencing \| 90% H2O/10% D2O	Resolution not provided
2RJV Crystal structure of the H41Y mutant of villin headpiece, P 21 21 21 space group Deposited 2007-10-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 760–826（67 aa） Fragment：HEADPIECE	Mutation：H791Y	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；PEG8000, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.45 Å R-free 0.206
2RJW The crystal structure of the H41Y mutant of villin headpiece, P61 SPACE GROUP. Deposited 2007-10-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 760–826（67 aa） Fragment：VILLIN HEADPIECE	Mutation：H791Y	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；PEG 8000, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.55 Å R-free 0.229
2RJW The crystal structure of the H41Y mutant of villin headpiece, P61 SPACE GROUP. Deposited 2007-10-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 760–826（67 aa） Fragment：VILLIN HEADPIECE	Mutation：H791Y	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；PEG 8000, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.55 Å R-free 0.229
2RJX Crystal structure of the headpiece domain of chicken villin, P61 space group Deposited 2007-10-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 760–826（67 aa） Fragment：VILLIN HEADPIECE	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；PEG 8000, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.70 Å R-free 0.240
2RJX Crystal structure of the headpiece domain of chicken villin, P61 space group Deposited 2007-10-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 760–826（67 aa） Fragment：VILLIN HEADPIECE	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；PEG 8000, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.70 Å R-free 0.240
2RJY Crystal structure of villin headpiece, P21 21 21 space group Deposited 2007-10-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 760–826（67 aa） Fragment：VILLIN HEADPIECE	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；PEG 8000, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.40 Å R-free 0.233
2VIK REFINED STRUCTURE OF THE ACTIN-SEVERING DOMAIN VILLIN 14T, DETERMINED BY SOLUTION NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1997-01-16	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–127（126 aa） Fragment：RESIDUES 1 - 126	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.15；298 K	Resolution not provided
2VIL REFINED STRUCTURE OF THE ACTIN-SEVERING DOMAIN VILLIN 14T, DETERMINED BY SOLUTION NMR, 11 STRUCTURES Deposited 1997-01-16	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–127（126 aa） Fragment：RESIDUES 1 - 126	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.15；298 K	Resolution not provided
3MYA Crystal Structure of HP67 H41F - P61 Deposited 2010-05-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 760–826（67 aa） Fragment：Villin Headpiece (unp residues 760-826)	Mutation：H41F	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Ammonium Sulfate, 0.1 M 2-morpholinoethanesulfonic Acid, 30% Polyethylene Glycol 8,000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.277
3MYA Crystal Structure of HP67 H41F - P61 Deposited 2010-05-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 760–826（67 aa） Fragment：Villin Headpiece (unp residues 760-826)	Mutation：H41F	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Ammonium Sulfate, 0.1 M 2-morpholinoethanesulfonic Acid, 30% Polyethylene Glycol 8,000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.277
3MYC Crystal Structure of HP67 H41F - P212121 Deposited 2010-05-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 760–826（67 aa） Fragment：Villin Headpiece (UNP residues 760-826)	Mutation：H41F	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Ammonium Sulfate, 0.1 M 2-Morphinoethanesulfonic acid, 30% Polyethyleneglycol 8,000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.70 Å R-free 0.216
3MYE Crystal Structure of HP67 L61GL Deposited 2010-05-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 760–826（67 aa） Fragment：Villin Headpiece (unp residues 760-826)	Mutation：L61GL	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.2 M Sodium Acetate, 0.1 M Cacodylate, 30% Polyethylene Glycol 10,000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.199
3NKJ Crystal Structure of HP67 L61G Deposited 2010-06-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 760–826（67 aa） Fragment：Villin Headpiece (UNP Residues 760-826)	Mutation：L811G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.2 M SODIUM ACETATE, 0.1 M CACODYLATE, 30% POLYETHYLENE GLYCOL 10,000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.60 Å R-free 0.219
3TJW Crystal Structure of Quasiracemic Villin Headpiece Subdomain Containing (F5Phe10) Substitution Deposited 2011-08-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 792–825（34 aa） Fragment：headpiece subdomain (UNP residues 792-825)	Mutation：N818H Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.75；298 K；2.0 M ammonium sulfate, 6% isopropanol, 8% glycerol, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.46 Å R-free 0.190
3TJW Crystal Structure of Quasiracemic Villin Headpiece Subdomain Containing (F5Phe10) Substitution Deposited 2011-08-25	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 792–825（34 aa） Fragment：headpiece subdomain (UNP residues 792-825)	Mutation：N818H Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.75；298 K；2.0 M ammonium sulfate, 6% isopropanol, 8% glycerol, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.46 Å R-free 0.190
3TRV Crystal structure of quasiracemic villin headpiece subdomain containing (F5Phe17) substitution Deposited 2011-09-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 792–826（35 aa） Fragment：headpiece subdomain (UNP residues 792-826)	Mutation：N818H Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2 IPA ISOPROPYL ALCOHOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.75；298 K；2.0 M ammonium sulfate, 6% isopropanol, 8% glycerol, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.00 Å R-free 0.155
3TRV Crystal structure of quasiracemic villin headpiece subdomain containing (F5Phe17) substitution Deposited 2011-09-11	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 792–826（35 aa） Fragment：headpiece subdomain (UNP residues 792-826)	Mutation：N818H Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.75；298 K；2.0 M ammonium sulfate, 6% isopropanol, 8% glycerol, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.00 Å R-free 0.155
3TRW Crystal structure of racemic villin headpiece subdomain crystallized in space group P-1 Deposited 2011-09-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 792–826（35 aa） Fragment：headpiece subdomain (UNP residues 792-826)	Mutation：N818H	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.75；298 K；2.0 M ammonium sulfate, 6% isopropanol, 8% glycerol, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.352
3TRW Crystal structure of racemic villin headpiece subdomain crystallized in space group P-1 Deposited 2011-09-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 792–826（35 aa） Fragment：headpiece subdomain (UNP residues 792-826)	Mutation：N818H	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.75；298 K；2.0 M ammonium sulfate, 6% isopropanol, 8% glycerol, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.352
4CZ3 HP24wt derived from the villin headpiece subdomain Deposited 2014-04-16	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 803–826（24 aa） Fragment：RESIDUES 803-826	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；288 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition 10% D2O/90% WATER	Resolution not provided
4CZ4 HP24stab derived from the villin headpiece subdomain Deposited 2014-04-16	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 803–826（24 aa） Fragment：RESIDUES 803-826	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；288 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition 10% D2O/90% WATER	Resolution not provided
5I1N Villin headpiece subdomain with a Gln26 to beta-3-homoglutamine substitution Deposited 2016-02-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 792–826（35 aa） Chain B 792–826（35 aa） Chain C 792–826（35 aa） Chain D 792–826（35 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；0.1 M sodium acetate pH 4.6, 1.5 M ammonium sulfate, 30% (v/v) PEG2000MME	Resolution 1.30 Å R-free 0.231
5I1O Villin headpiece subdomain with a Gln26 to ACPC substitution Deposited 2016-02-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 792–826（35 aa） Chain B 792–826（35 aa） Chain C 792–826（35 aa） Chain D 792–826（35 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；0.1 M Tris-HCl pH 8.5, 0.1 M sodium acetate, 30% (w/v) PEG 4000	Resolution 1.35 Å R-free 0.204
5I1P Villin headpiece subdomain with a Lys30 to beta-3-homolysine substitution Deposited 2016-02-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 792–826（35 aa） Chain B 792–826（35 aa） Chain C 792–826（35 aa） Chain D 792–826（35 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	EOH ETHANOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；0.1 M Tris-HCl pH 8.5, 20% (v/v) ethanol	Resolution 1.40 Å R-free 0.235
5I1S Villin headpiece subdomain with a Lys30 to APC substitution Deposited 2016-02-05	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 A 792–826（35 aa） Chain B 792–826（35 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；0.1 M sodium acetate pH 4.6, 1.5 M ammonium sulfate, 30% (v/v) PEG2000MME	Resolution 1.12 Å R-free 0.185
9MF7 Backbone alpha-Methylation in the Villin Headpiece Miniprotein: Prototype HP35 Deposited 2024-12-09	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 792–826（35 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；293 K；Ionic strength (raw mmCIF value) 10；Pressure 1 NMR sample composition 0.52 mM Villin-1 headpiece: Met12Nle, 0.21 mM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
9MF8 Backbone alpha-Methylation in the Villin Headpiece Miniprotein: HP35 with Aib at Position 15 Deposited 2024-12-09	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 792–826（35 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；288 K；Ionic strength (raw mmCIF value) 10；Pressure 1 NMR sample composition 0.47 mM Villin-1 headpiece: Met12Nle, Ser15Aib, 0.15 mM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
9MF9 Backbone alpha-Methylation in the Villin Headpiece Miniprotein: HP35 with Calpha-methyl-Ser at Position 15 Deposited 2024-12-09	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 792–826（35 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；288 K；Ionic strength (raw mmCIF value) 10；Pressure 1 NMR sample composition 0.44 mM Villin-1 headpiece: Met12Nle, Ser15alphaMeSer, 0.15 mM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
9MFA Backbone alpha-Methylation in the Villin Headpiece Miniprotein: HP35 with Aib at Position 30 Deposited 2024-12-09	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 792–826（35 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；288 K；Ionic strength (raw mmCIF value) 10；Pressure 1 NMR sample composition 0.59 mM Villin-1 headpiece: Met12Nle, Lys30Aib, 0.15 mM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
9MFB Backbone alpha-Methylation in the Villin Headpiece Miniprotein: HP35 with Calpha-methyl-Lys at Position 30 Deposited 2024-12-09	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 792–826（35 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；288 K；Ionic strength (raw mmCIF value) 10；Pressure 1 NMR sample composition 0.53 mM Villin-1 headpiece: Met12Nle, Lys30alphaMeLys, 0.15 mM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
9YLZ Backbone Modification in the Villin Headpiece Miniprotein: HP35 with beta3Leu at Position 28 Deposited 2025-10-09	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 792–826（35 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.1；283 K；Ionic strength (raw mmCIF value) 10；Pressure 1 NMR sample composition 0.96 mM Villin-1 headpiece: Met12Nle, Leu28beta3Leu, 0.2 mM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
9YM0 Backbone Modification in the Villin Headpiece Miniprotein: HP35 with ACPC at Position 28 Deposited 2025-10-09	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 792–826（35 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.9；288 K；Ionic strength (raw mmCIF value) 10；Pressure 1 NMR sample composition 0.91 mM Villin-1 headpiece: Met12Nle, Leu28ACPC, 0.2 mM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
9YM1 Backbone Modification in the Villin Headpiece Miniprotein: HP35 with beta3Lys at Position 29 Deposited 2025-10-09	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 792–826（35 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；278 K；Ionic strength (raw mmCIF value) 10；Pressure 1 NMR sample composition 0.89 mM Villin-1 headpiece: Met12Nle, Lys29beta3Lys, 0.2 mM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
9YM2 Backbone Modification in the Villin Headpiece Miniprotein: HP35 with ACPC at Position 29 Deposited 2025-10-09	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 792–826（35 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.8；278 K；Ionic strength (raw mmCIF value) 10；Pressure 1 NMR sample composition 1.0 mM Villin-1 headpiece: Met12Nle, Lys29ACPC, 0.2 mM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
9YM3 Backbone Modification in the Villin Headpiece Miniprotein: HP35 with ACPC at Position 30 Deposited 2025-10-09	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 792–826（35 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；288 K；Ionic strength (raw mmCIF value) 10；Pressure 1 NMR sample composition 1.0 mM Villin-1 headpiece: Met12Nle, Lys30ACPC, 0.2 mM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
9YM4 Backbone Modification in the Villin Headpiece Miniprotein: HP35 with beta3Phe at Position 6 Deposited 2025-10-09	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 792–826（35 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.8；278 K；Ionic strength (raw mmCIF value) 10；Pressure 1 NMR sample composition 1.0 mM Villin-1 headpiece: Met12Nle, Phe6beta3Phe, 0.2 mM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
9YM5 Backbone Modification in the Villin Headpiece Miniprotein: HP35 with Calpha-methyl-Phe at Position 6 Deposited 2025-10-09	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 792–826（35 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.7；293 K；Ionic strength (raw mmCIF value) 10；Pressure 1 NMR sample composition 1.0 mM Villin-1 headpiece: Met12Nle, Phe6alphaMePhe, 0.2 mM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
9YM6 Backbone Modification in the Villin Headpiece Miniprotein: HP35 with Calpha-methyl-Phe at Position 17 Deposited 2025-10-09	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 792–826（35 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；288 K；Ionic strength (raw mmCIF value) 10；Pressure 1 NMR sample composition 1.0 mM Villin-1 headpiece: Met12Nle, Phe17alphaMePhe, 0.2 mM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

45 other PDB entries and 51 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VILI_CHICK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–35； UniProt 792–826

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3try
Deposition date deposition_date	2011-09-11
Structure title title	Crystal structure of racemic villin headpiece subdomain in space group I-4c2
Keywords keywords	racemate, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	10.81 Å
Radius of gyration Rg (electron density) rg_electron	9.36 Å
Forward intensity I(0) i0	381629.00
Molecular weight molecular_weight	4047.0 kDa
Excluded volume excluded_volume	5212 Å³
Envelope volume envelope_volume	5429 Å³
Hydration-shell volume shell_volume	5455 Å³
Envelope diameter envelope_diameter	31.8 Å
Shell Rg shell_rg	13.88 Å
Envelope Rg envelope_rg	9.57 Å
Shape Rg shape_rg	9.34 Å
Total Rg total_rg	10.92 Å
Total atoms total_atoms	282
Residues n_residues	2
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	35.1 Å
Rg (real space) rg_real	10.77 Å
Rg uncertainty (real space) rg_real_error	0.26 Å
I(0) (real space) i0_real	3.8160e+05
I(0) uncertainty (real space) i0_real_error	3.7600e+03
Rg (reciprocal space) rg_reciprocal	10.77 Å
I(0) (reciprocal space) i0_reciprocal	381600.0000
Solution quality estimate total_estimate	0.8972
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	14.7 Å
Skewness Skewness skewness	0.130
Kurtosis Kurtosis kurtosis	-0.387
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	22910.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.909; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.946

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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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8. Citations (1)

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Unit-cell length a length_a	63.128 Å
Unit-cell length b length_b	63.128 Å
Unit-cell length c length_c	39.135 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	I -4 c 2
Space-group number int_tables_number	120
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	22.319 Å
R factor r_factor	0.2019
R_work r_work	0.2005
R_free r_free	0.2301

Description description	D-Villin-1
Molecular weight formula_weight	4083.7 kDa
Mutation mutation	N818H
Source method src_method	syn
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	285

Crystal structure of racemic villin headpiece subdomain in space group I-4c2

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

D-Villin-1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	3

fit	/app/data/saxs_computation/tr/3try/3try.fit
pddf	/app/data/pr_computation/tr/3try/3try.pr.out
profile	/app/data/saxs_computation/tr/3try/3try.dat