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- PDB-5ou7: Crystal structure of the Glycoprotein VI loop truncation mutant P... -

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Basic information

Entry
Database: PDB / ID: 5ou7
TitleCrystal structure of the Glycoprotein VI loop truncation mutant PAVS-PAPYKN
ComponentsPlatelet glycoprotein VI
KeywordsBLOOD CLOTTING / Platelet / glycoprotein / GPVI / collagen-binding / platelet activation
Function / homology
Function and homology information


tetraspanin-enriched microdomain / collagen-activated signaling pathway / Platelet Adhesion to exposed collagen / positive regulation of platelet aggregation / enzyme-linked receptor protein signaling pathway / GPVI-mediated activation cascade / collagen binding / protein tyrosine kinase binding / Cell surface interactions at the vascular wall / platelet activation ...tetraspanin-enriched microdomain / collagen-activated signaling pathway / Platelet Adhesion to exposed collagen / positive regulation of platelet aggregation / enzyme-linked receptor protein signaling pathway / GPVI-mediated activation cascade / collagen binding / protein tyrosine kinase binding / Cell surface interactions at the vascular wall / platelet activation / transmembrane signaling receptor activity / signaling receptor activity / membrane raft / cell surface / extracellular exosome / plasma membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like ...Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-PG6 / PHOSPHATE ION / Platelet glycoprotein VI
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFeitsma, L.J. / Huizinga, E.G.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organization for Scientific ResearchECHO 700.58.006 Netherlands
CitationJournal: To Be Published
Title: Structural insights into collagen-binding by platelet receptor Glycoprotein VI
Authors: Feitsma, L.J. / Brondijk, T.H.C. / Jarvis, G. / Hagemans, D. / Bihan, D. / Jerah, N. / Versteeg, M. / Farndale, R.W. / Huizinga, E.G.
History
DepositionAug 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Platelet glycoprotein VI
B: Platelet glycoprotein VI
C: Platelet glycoprotein VI
D: Platelet glycoprotein VI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,98126
Polymers78,8774
Non-polymers2,10422
Water6,197344
1
A: Platelet glycoprotein VI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4799
Polymers19,7191
Non-polymers7608
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Platelet glycoprotein VI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4799
Polymers19,7191
Non-polymers7608
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Platelet glycoprotein VI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0114
Polymers19,7191
Non-polymers2923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Platelet glycoprotein VI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0114
Polymers19,7191
Non-polymers2923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.650, 44.050, 117.660
Angle α, β, γ (deg.)90.00, 104.69, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12D
22C

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: 2

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYBB2 - 1744 - 176
21GLYGLYAA2 - 1744 - 176
12ALAALADD2 - 1794 - 181
22ALAALACC2 - 1794 - 181

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999998, 0.000885, -0.001835), (0.000886, 0.999999, -0.000759), (0.001835, -0.000761, -0.999998)-103.05657, -3.93706, -56.82741
3given(1), (1), (1)
4given(-0.999995, -0.001239, 0.002865), (-0.001232, 0.999996, 0.00243), (-0.002868, 0.002427, -0.999993)-103.07332, -3.91525, -56.8208

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Platelet glycoprotein VI / GPVI / Glycoprotein 6


Mass: 19719.215 Da / Num. of mol.: 4 / Mutation: -102-105 -131-136
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GP6 / Cell line (production host): HEK293-EBNA1-S / Production host: Homo sapiens (human) / References: UniProt: Q9HCN6
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 362 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE / Polyethylene glycol


Mass: 266.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O6
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.1 M phosphate-citrate buffer pH 4.0 40% (v/v) PEG-300

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.9→113.81 Å / Num. obs: 58873 / % possible obs: 95.1 % / Redundancy: 2.1 % / Biso Wilson estimate: 25.6 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.081 / Net I/σ(I): 5
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 2.1 % / Rmerge(I) obs: 1.08 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3656 / CC1/2: 0.62 / % possible all: 93.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
iMOSFLM1.0.7data reduction
Aimless0.1.30data scaling
PHASER2.7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GI7

2gi7


Resolution: 1.9→113.81 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 10.313 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.169 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25967 2967 5 %RANDOM
Rwork0.22117 ---
obs0.22309 55826 94.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.189 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å2-0 Å20.06 Å2
2---0.48 Å20 Å2
3---0.93 Å2
Refinement stepCycle: 1 / Resolution: 1.9→113.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5426 0 112 344 5882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.025945
X-RAY DIFFRACTIONr_bond_other_d0.0010.025615
X-RAY DIFFRACTIONr_angle_refined_deg1.482.0048148
X-RAY DIFFRACTIONr_angle_other_deg0.779313009
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0325770
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.02522.259239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43515943
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7371552
X-RAY DIFFRACTIONr_chiral_restr0.0890.2888
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216648
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021348
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9842.6212876
X-RAY DIFFRACTIONr_mcbond_other1.9822.6212875
X-RAY DIFFRACTIONr_mcangle_it3.3143.9163606
X-RAY DIFFRACTIONr_mcangle_other3.3143.9163607
X-RAY DIFFRACTIONr_scbond_it2.2012.9783069
X-RAY DIFFRACTIONr_scbond_other2.2012.9783069
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6054.3464507
X-RAY DIFFRACTIONr_long_range_B_refined6.22521.7936279
X-RAY DIFFRACTIONr_long_range_B_other6.13921.5286182
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1838medium positional0.710.5
22C1678medium positional0.420.5
11A1029tight thermal0.570.5
22C1039tight thermal1.370.5
11A1838medium thermal1.432
22C1678medium thermal1.882
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 190 -
Rwork0.388 3987 -
obs--92.62 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3153-0.24820.14940.6745-0.10640.0767-0.00290.0255-0.0074-0.044-0.015-0.0431-0.0060.01530.01790.0065-0.0023-0.00640.00380.0110.0883-33.3152-4.2205-8.0809
20.32180.27440.13810.79310.1640.0663-0.0073-0.0408-0.02110.0499-0.00580.0404-0.0007-0.01810.01320.00710.0056-0.0030.0093-0.00940.0912-69.7232-8.1676-48.8131
31.0753-0.094-0.3140.2655-0.1110.1677-0.05560.15450.0569-0.07460.0414-0.03030.0597-0.07620.01420.0289-0.0213-0.00360.044-0.03170.10598.419-16.5085-17.69
41.16810.0835-0.29420.12630.06610.1376-0.0561-0.13990.01190.03770.02360.03810.0440.05740.03250.02320.0177-0.00860.03560.02210.1098-111.5443-20.4611-39.1851
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 174
2X-RAY DIFFRACTION2B2 - 174
3X-RAY DIFFRACTION3C2 - 179
4X-RAY DIFFRACTION4D2 - 179

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