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2jm0

Solution structure of chicken villin headpiece subdomain containing a fluorinated side chain in the core

Method: SOLUTION NMR Dmax: 33.3 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Villin-1

OrganismNot specified

UniProt P02640

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：residues 792-826 Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer 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

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 2JM0 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 experimental conditions 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 experimental conditions 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 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：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 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：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 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：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 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：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 experimental method 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 experimental method 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 experimental method 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 mutation/modification 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
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
2LLF Sixth Gelsolin-like domain of villin in 5 mM CaCl2 Deposited 2011-11-07 Different construct Different mutation/modification Different experimental conditions 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 experimental conditions 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 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：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 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：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 experimental method 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 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：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 experimental method 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 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：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 experimental conditions 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 experimental conditions 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 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：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 experimental method 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 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：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 experimental method 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 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：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 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 792–825（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 mutation/modification Different ligand/ion Different experimental method 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 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：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 construct Different mutation/modification Different ligand/ion Different experimental method 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 construct Different mutation/modification 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：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 construct Different mutation/modification Different experimental method 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
3TRY Crystal structure of racemic villin headpiece subdomain in space group I-4c2 Deposited 2011-09-11 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：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
4CZ3 HP24wt derived from the villin headpiece subdomain Deposited 2014-04-16 Different construct Different experimental conditions 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 experimental conditions 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 experimental method 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 experimental method 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 method 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 experimental method 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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 experimental conditions 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

SAXS profile for 2jm0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2jm0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2jm0
Deposition date deposition_date2006-09-06
Structure title titleSolution structure of chicken villin headpiece subdomain containing a fluorinated side chain in the core
Keywords keywordsfluorinated Phe, VHP, chicken villin headpiece, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier9.12 Å
Radius of gyration Rg (electron density) rg_electron9.21 Å
Forward intensity I(0) i0112981000.00
Molecular weight molecular_weight86878.0 kDa
Excluded volume excluded_volume107260 ų
Envelope volume envelope_volume7742 ų
Hydration-shell volume shell_volume6972 ų
Envelope diameter envelope_diameter32.7 Å
Shell Rg shell_rg14.98 Å
Envelope Rg envelope_rg10.16 Å
Shape Rg shape_rg9.15 Å
Total Rg total_rg9.57 Å
Total atoms total_atoms11700
Residues n_residues660
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 dmax33.3 Å
Rg (real space) rg_real9.07 Å
Rg uncertainty (real space) rg_real_error0.40 Å
I(0) (real space) i0_real1.1300e+08
I(0) uncertainty (real space) i0_real_error1.1810e+06
Rg (reciprocal space) rg_reciprocal9.07 Å
I(0) (reciprocal space) i0_reciprocal113000000.0000
Solution quality estimate total_estimate0.5950
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary12.6 Å
Skewness Skewness skewness-0.011
Kurtosis Kurtosis kurtosis-0.588
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11700.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.689; Stabil: 0.989; Sysdev: 0.256; Positv: 1.000; Valcen: 0.927; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)