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- PDB-4yr6: Fab fragment of 5G6 in complex with epitope peptide -

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Basic information

Entry
Database: PDB / ID: 4yr6
TitleFab fragment of 5G6 in complex with epitope peptide
Components
  • ACE-LYS-LEU-ARG-GLY-VAL-LEU-GLN-GLY-HIS-LEU
  • heavy chain of 5G6
  • light chain of 5G6
KeywordsIMMUNE SYSTEM / GPIBA shedding inhibitor / 5G6 / KL10
Function / homology
Function and homology information


thrombin-activated receptor activity / glycoprotein Ib-IX-V complex / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / positive regulation of leukocyte tethering or rolling / blood coagulation, intrinsic pathway / Defective F9 activation / Platelet Adhesion to exposed collagen / positive regulation of platelet activation / megakaryocyte development ...thrombin-activated receptor activity / glycoprotein Ib-IX-V complex / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / positive regulation of leukocyte tethering or rolling / blood coagulation, intrinsic pathway / Defective F9 activation / Platelet Adhesion to exposed collagen / positive regulation of platelet activation / megakaryocyte development / GP1b-IX-V activation signalling / regulation of blood coagulation / Platelet Aggregation (Plug Formation) / release of sequestered calcium ion into cytosol / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / extracellular matrix / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / cell morphogenesis / platelet activation / blood coagulation / cell surface receptor signaling pathway / cell adhesion / external side of plasma membrane / cell surface / extracellular space / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Leucine-rich repeats, bacterial type / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. ...Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Leucine-rich repeats, bacterial type / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Platelet glycoprotein Ib alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsTao, Y. / Mo, X. / Li, R.
Funding support China, 2items
OrganizationGrant numberCountry
China Natural Science Fund81100346 China
Shanghai Xinyouqing ProgramXYQ2013069 China
CitationJournal: Sci Rep / Year: 2016
Title: Structural basis for the specific inhibition of glycoprotein Ib alpha shedding by an inhibitory antibody.
Authors: Tao, Y. / Zhang, X. / Liang, X. / Zang, J. / Mo, X. / Li, R.
History
DepositionMar 14, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Source and taxonomy
Revision 1.2May 13, 2020Group: Database references / Category: citation / citation_author
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
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: heavy chain of 5G6
B: light chain of 5G6
C: ACE-LYS-LEU-ARG-GLY-VAL-LEU-GLN-GLY-HIS-LEU
D: heavy chain of 5G6
E: light chain of 5G6
F: ACE-LYS-LEU-ARG-GLY-VAL-LEU-GLN-GLY-HIS-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9948
Polymers96,8106
Non-polymers1842
Water5,224290
1
A: heavy chain of 5G6
B: light chain of 5G6
C: ACE-LYS-LEU-ARG-GLY-VAL-LEU-GLN-GLY-HIS-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4974
Polymers48,4053
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-36 kcal/mol
Surface area19560 Å2
MethodPISA
2
D: heavy chain of 5G6
E: light chain of 5G6
F: ACE-LYS-LEU-ARG-GLY-VAL-LEU-GLN-GLY-HIS-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4974
Polymers48,4053
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-35 kcal/mol
Surface area19010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.900, 147.060, 194.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11E-435-

HOH

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Components

#1: Antibody heavy chain of 5G6


Mass: 23563.564 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody light chain of 5G6


Mass: 23692.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein/peptide ACE-LYS-LEU-ARG-GLY-VAL-LEU-GLN-GLY-HIS-LEU


Mass: 1149.410 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P07359*PLUS
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.78 Å3/Da / Density % sol: 67.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1.6M (NH4)2SO4, 0.01M NiCl2, 0.1M Tris, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 57791 / % possible obs: 98.3 % / Redundancy: 7.1 % / Net I/σ(I): 15.3

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
PHENIXmodel building
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U9U

3u9u


Resolution: 2.38→45.154 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2511 2956 5.08 %
Rwork0.2115 --
obs0.2135 55282 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.38→45.154 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6606 0 12 290 6908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096797
X-RAY DIFFRACTIONf_angle_d1.2239261
X-RAY DIFFRACTIONf_dihedral_angle_d14.5022363
X-RAY DIFFRACTIONf_chiral_restr0.0831065
X-RAY DIFFRACTIONf_plane_restr0.0051168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.4190.2841400.25362542X-RAY DIFFRACTION96
2.419-2.46070.3291380.252540X-RAY DIFFRACTION97
2.4607-2.50550.36761260.24892559X-RAY DIFFRACTION97
2.5055-2.55370.29621190.24662612X-RAY DIFFRACTION97
2.5537-2.60580.29411440.24382559X-RAY DIFFRACTION99
2.6058-2.66240.29781380.24612592X-RAY DIFFRACTION98
2.6624-2.72440.27291370.24652623X-RAY DIFFRACTION99
2.7244-2.79250.31751380.2522635X-RAY DIFFRACTION99
2.7925-2.8680.3511380.24662617X-RAY DIFFRACTION99
2.868-2.95230.30221370.24762605X-RAY DIFFRACTION99
2.9523-3.04760.31971400.2412644X-RAY DIFFRACTION99
3.0476-3.15650.30651440.23792641X-RAY DIFFRACTION100
3.1565-3.28290.26871400.23122656X-RAY DIFFRACTION100
3.2829-3.43220.28471450.22282654X-RAY DIFFRACTION100
3.4322-3.61310.271570.20142621X-RAY DIFFRACTION100
3.6131-3.83940.25531480.19082654X-RAY DIFFRACTION100
3.8394-4.13560.18991450.18032664X-RAY DIFFRACTION100
4.1356-4.55140.17671290.15652651X-RAY DIFFRACTION98
4.5514-5.20920.17441360.15662671X-RAY DIFFRACTION99
5.2092-6.55980.22761420.20952726X-RAY DIFFRACTION100
6.5598-45.16180.25621750.24052800X-RAY DIFFRACTION99

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