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- PDB-7jik: Human recombinant Beta-2-Glycoprotein 1 -

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Basic information

Entry
Database: PDB / ID: 7jik
TitleHuman recombinant Beta-2-Glycoprotein 1
ComponentsBeta-2-glycoprotein 1
KeywordsBLOOD CLOTTING / Plasma protein / antibody binding / antiphospholipid syndrome
Function / homology
Function and homology information


lipoprotein lipase activator activity / triglyceride transport / platelet dense granule lumen / positive regulation of lipoprotein lipase activity / negative regulation of complement activation, classical pathway / blood coagulation, intrinsic pathway / T cell mediated immunity / negative regulation of myeloid cell apoptotic process / chylomicron / regulation of fibrinolysis ...lipoprotein lipase activator activity / triglyceride transport / platelet dense granule lumen / positive regulation of lipoprotein lipase activity / negative regulation of complement activation, classical pathway / blood coagulation, intrinsic pathway / T cell mediated immunity / negative regulation of myeloid cell apoptotic process / chylomicron / regulation of fibrinolysis / very-low-density lipoprotein particle / negative regulation of blood coagulation / high-density lipoprotein particle / negative regulation of endothelial cell migration / triglyceride metabolic process / plasminogen activation / negative regulation of endothelial cell proliferation / negative regulation of smooth muscle cell apoptotic process / positive regulation of blood coagulation / negative regulation of fibrinolysis / negative regulation of angiogenesis / phospholipid binding / Platelet degranulation / heparin binding / collagen-containing extracellular matrix / lipid binding / cell surface / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Beta-2-glycoprotein-1 fifth domain / Beta-2-glycoprotein-1 fifth domain / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily
Similarity search - Domain/homology
Beta-2-glycoprotein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsKlenotic, P.A. / Yu, E.W.Y.
CitationJournal: To Be Published
Title: Beta-2-Glycoprotein I and it's role in APS
Authors: Klenotic, P.A. / Yu, E.W.Y.
History
DepositionJul 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: Beta-2-glycoprotein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0455
Polymers36,3001
Non-polymers1,7464
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)159.645, 172.976, 113.439
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Beta-2-glycoprotein 1 / APC inhibitor / Activated protein C-binding protein / Anticardiolipin cofactor / Apolipoprotein H / ...APC inhibitor / Activated protein C-binding protein / Anticardiolipin cofactor / Apolipoprotein H / Apo-H / Beta-2-glycoprotein I / Beta(2)GPI


Mass: 36299.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOH, B2G1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P02749
#2: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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
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

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 100mM Hepes, pH 7.5, 1.8M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. obs: 43781 / % possible obs: 99.7 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.216 / Rpim(I) all: 0.08 / Rrim(I) all: 0.231 / Χ2: 1 / Net I/σ(I): 7 / Num. measured all: 365257
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.69-2.798.83.10843000.2811.1023.3011100
2.79-2.98.82.11643380.4060.7512.2481.001100
2.9-3.038.51.47743580.5950.5331.5731.001100
3.03-3.198.10.82843430.8110.3040.8831.00199.8
3.19-3.397.80.48843540.9150.1820.5220.99999.9
3.39-3.659.10.3443600.9590.1190.361199.9
3.65-4.028.70.24443740.9650.0880.259199.9
4.02-4.67.90.18543750.9680.0720.199199.3
4.6-5.797.70.14344020.9770.0570.1540.99998.9
5.79-5080.09245770.9930.0350.0990.99999.5

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Cootmodel building
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QUB

1qub


Resolution: 2.69→48.93 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2383 2013 4.6 %
Rwork0.221 41736 -
obs0.2218 43749 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 180.23 Å2 / Biso mean: 89.694 Å2 / Biso min: 44.22 Å2
Refinement stepCycle: final / Resolution: 2.69→48.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2496 0 115 0 2611
Biso mean--133.91 --
Num. residues----321
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.69-2.760.39291380.382629283066100
2.76-2.830.41541430.363629533096100
2.83-2.920.42481420.381829693111100
2.92-3.010.34541360.362129613097100
3.01-3.120.35271450.298529423087100
3.12-3.240.31581400.287229783118100
3.24-3.390.26911390.267129693108100
3.39-3.570.26271490.247829843133100
3.57-3.790.23181480.20829683116100
3.79-4.080.2091350.187629983133100
4.08-4.490.19611390.167229723111100
4.49-5.140.17241390.15622986312599
5.14-6.480.18771480.18813003315199
6.48-48.930.24491720.222931253297100
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)
12.713-0.8637-2.37260.6210.58983.69730.0594-0.2157-0.2297-0.0209-0.22990.01350.35530.25880.19960.7632-0.05780.01840.71630.02020.6973235.0879227.3758153.4604
22.40071.77461.58331.39471.21933.6234-0.16980.15790.0689-0.20430.1782-0.0212-0.54120.4036-0.05040.6037-0.00760.02410.58710.01510.5865167.7754158.24692.2601
31.23870.2181-0.09780.86861.14853.9545-0.0154-0.09220.1466-0.1880.006-0.0682-0.37310.25790.03460.6079-0.1249-0.03320.63230.02810.7156174.8555195.2928120.6346
42.31441.95623.14920.38811.51771.43350.1548-0.73030.0547-0.0229-0.392-0.0120.0382-0.62660.25880.8955-0.3621-0.04631.1987-0.19340.8732194.2965220.8612155.0984
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 241 through 326 )A241 - 326
2X-RAY DIFFRACTION2chain 'A' and (resid 1 through 61 )A1 - 61
3X-RAY DIFFRACTION3chain 'A' and (resid 62 through 149 )A62 - 149
4X-RAY DIFFRACTION4chain 'A' and (resid 150 through 240 )A150 - 240

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