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- PDB-7a6o: Crystal Structure of the Complex of the Recombinant Von Willebran... -

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Basic information

Entry
Database: PDB / ID: 7a6o
TitleCrystal Structure of the Complex of the Recombinant Von Willebrand Factor AIM-A1 domain and VHH81 at 2.1 Angstrom resolution
Components
  • VHH81 Nanobody fragment
  • von Willebrand factor
KeywordsBLOOD CLOTTING / Thrombosis Von Willebrand Factor A1 Aim-A1 Blood Clotting Complex VWF
Function / homology
Function and homology information


blood coagulation / extracellular region
Similarity search - Function
von Willebrand factor, VWA N-terminal domain / Von Willebrand factor / VWA N-terminal / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain ...von Willebrand factor, VWA N-terminal domain / Von Willebrand factor / VWA N-terminal / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain / von Willebrand factor (vWF) type C domain / Trypsin Inhibitor-like, cysteine rich domain / Serine protease inhibitor-like superfamily / Trypsin Inhibitor like cysteine rich domain / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
von Willebrand factor
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.117 Å
AuthorsBrown, A.K. / Emsley, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
British Heart FoundationFS/18/70/33893 United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: Activation of von Willebrand factor via mechanical unfolding of its discontinuous autoinhibitory module.
Authors: Arce, N.A. / Cao, W. / Brown, A.K. / Legan, E.R. / Wilson, M.S. / Xu, E.R. / Berndt, M.C. / Emsley, J. / Zhang, X.F. / Li, R.
History
DepositionAug 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Data collection / Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / refine / reflns / reflns_shell
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _refine.ls_d_res_high / _reflns.d_resolution_high / _reflns_shell.d_res_high
Revision 2.0Jul 28, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence / Refinement description / Structure summary
Category: atom_site / entity_poly ...atom_site / entity_poly / pdbx_database_status / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine_hist / struct_conf / struct_conn / struct_ref_seq / struct_sheet_range
Item: _atom_site.auth_asym_id / _entity_poly.pdbx_strand_id ..._atom_site.auth_asym_id / _entity_poly.pdbx_strand_id / _pdbx_database_status.pdb_format_compatible / _pdbx_distant_solvent_atoms.auth_asym_id / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_special_symmetry.auth_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_peptide_omega.auth_asym_id_1 / _pdbx_validate_peptide_omega.auth_asym_id_2 / _pdbx_validate_rmsd_angle.auth_asym_id_1 / _pdbx_validate_rmsd_angle.auth_asym_id_2 / _pdbx_validate_rmsd_angle.auth_asym_id_3 / _pdbx_validate_torsion.auth_asym_id / _refine_hist.d_res_high / _struct_conf.beg_auth_asym_id / _struct_conf.end_auth_asym_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_ref_seq.pdbx_strand_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.end_auth_asym_id
Revision 2.1Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: von Willebrand factor
B: VHH81 Nanobody fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4003
Polymers37,3042
Non-polymers961
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-16 kcal/mol
Surface area15090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.234, 65.234, 233.231
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1696-

HOH

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Components

#1: Protein von Willebrand factor /


Mass: 23447.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VWF / Plasmid: pET22b+ / Production host: Homo sapiens (human) / Strain (production host): Expi293F / References: UniProt: L8E853
#2: Antibody VHH81 Nanobody fragment


Mass: 13856.432 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Gene: VHH / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 62.98 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 5.2 / Details: 3.2 M ammonium sulphate, 0.08 M sodium citrate

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Data collection

DiffractionMean temperature: 283 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.117→62.9 Å / Num. obs: 19344 / % possible obs: 92.4 % / Redundancy: 5.2 % / CC1/2: 1 / Rmerge(I) obs: 0.048 / Net I/σ(I): 15.1
Reflection shellResolution: 2.117→2.3 Å / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2527 / CC1/2: 0.6 / % possible all: 69.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AUQ

1auq


Resolution: 2.117→62.8 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.916 / Cross valid method: FREE R-VALUE / ESU R: 0.3 / ESU R Free: 0.247
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2558 921 4.761 %
Rwork0.1947 18423 -
all0.198 --
obs-19344 92.4 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 51.291 Å2
Baniso -1Baniso -2Baniso -3
1--0.155 Å20 Å20 Å2
2---0.155 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.117→62.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2620 0 5 160 2785
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132683
X-RAY DIFFRACTIONr_bond_other_d0.0350.0172540
X-RAY DIFFRACTIONr_angle_refined_deg1.7271.6453626
X-RAY DIFFRACTIONr_angle_other_deg2.3391.5755873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.555333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.91320.333150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.49915473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8671528
X-RAY DIFFRACTIONr_chiral_restr0.070.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023002
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02598
X-RAY DIFFRACTIONr_nbd_refined0.2110.2494
X-RAY DIFFRACTIONr_symmetry_nbd_other0.220.22427
X-RAY DIFFRACTIONr_nbtor_refined0.1620.21229
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.21251
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2131
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1330.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.5690.23
X-RAY DIFFRACTIONr_nbd_other0.1540.218
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3870.29
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2780.21
X-RAY DIFFRACTIONr_mcbond_it4.2655.1611332
X-RAY DIFFRACTIONr_mcbond_other4.2655.1571331
X-RAY DIFFRACTIONr_mcangle_it5.9377.7241662
X-RAY DIFFRACTIONr_mcangle_other5.9357.7281663
X-RAY DIFFRACTIONr_scbond_it5.2445.6621351
X-RAY DIFFRACTIONr_scbond_other5.2115.6521347
X-RAY DIFFRACTIONr_scangle_it7.9148.2791963
X-RAY DIFFRACTIONr_scangle_other7.888.2641958
X-RAY DIFFRACTIONr_lrange_it24.82260.262883
X-RAY DIFFRACTIONr_lrange_other24.86460.0482862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.117-2.1720.64810.44930X-RAY DIFFRACTION1.4372
2.172-2.2310.537120.376224X-RAY DIFFRACTION11.4065
2.231-2.2960.308220.299397X-RAY DIFFRACTION20.449
2.296-2.3670.423280.306522X-RAY DIFFRACTION27.6104
2.367-2.4440.296230.274640X-RAY DIFFRACTION34.4774
2.444-2.530.296350.249811X-RAY DIFFRACTION44.9522
2.53-2.6260.337480.271062X-RAY DIFFRACTION61.2245
2.626-2.7330.327560.2691441X-RAY DIFFRACTION85.6407
2.733-2.8540.348780.2491561X-RAY DIFFRACTION97.6758
2.854-2.9940.308770.251527X-RAY DIFFRACTION99.3804
2.994-3.1560.287810.241427X-RAY DIFFRACTION99.2105
3.156-3.3470.265740.2331380X-RAY DIFFRACTION99.1138
3.347-3.5780.306660.2231306X-RAY DIFFRACTION98.9185
3.578-3.8650.298630.2061217X-RAY DIFFRACTION98.5373
3.865-4.2330.23650.1691099X-RAY DIFFRACTION98.0623
4.233-4.7330.178460.1271045X-RAY DIFFRACTION99.1818
4.733-5.4650.167510.13918X-RAY DIFFRACTION99.1812
5.465-6.6920.208480.159793X-RAY DIFFRACTION99.2916
6.692-9.460.256310.161634X-RAY DIFFRACTION98.3728

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