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- PDB-6xsd: Patient-derived B2GPI -

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Basic information

Entry
Database: PDB / ID: 6xsd
TitlePatient-derived B2GPI
ComponentsBeta-2-glycoprotein 1
KeywordsBLOOD CLOTTING / Plasma protein / antibody binding / antiphospholipid syndrome
Function / homology
Function and homology information


positive regulation of triglyceride metabolic process / triglyceride transport / lipoprotein lipase activator activity / chylomicron remodeling / platelet dense granule lumen / lipase binding / blood coagulation, intrinsic pathway / very-low-density lipoprotein particle remodeling / regulation of fibrinolysis / negative regulation of myeloid cell apoptotic process ...positive regulation of triglyceride metabolic process / triglyceride transport / lipoprotein lipase activator activity / chylomicron remodeling / platelet dense granule lumen / lipase binding / blood coagulation, intrinsic pathway / very-low-density lipoprotein particle remodeling / regulation of fibrinolysis / negative regulation of myeloid cell apoptotic process / chylomicron / high-density lipoprotein particle / very-low-density lipoprotein particle / negative regulation of endothelial cell migration / plasminogen activation / negative regulation of endothelial cell proliferation / negative regulation of smooth muscle cell apoptotic process / negative regulation of blood coagulation / positive regulation of blood coagulation / negative regulation of fibrinolysis / negative regulation of angiogenesis / phospholipid binding / Platelet degranulation / heparin binding / : / lipid binding / cell surface / extracellular space / extracellular exosome / extracellular region / identical protein binding
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: 2.54 Å
AuthorsKlenotic, P.A. / Yu, E.W.Y.
CitationJournal: To Be Published
Title: B2-Glycoprotein I and it's role in APS
Authors: Klenotic, P.A. / Yu, E.W.Y.
History
DepositionJul 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)37,5915
Polymers36,3001
Non-polymers1,2914
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)159.463, 167.566, 114.161
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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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 natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02749
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: 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
Has protein modificationY

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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: 0.98 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: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.54→50 Å / Num. obs: 50299 / % possible obs: 99.9 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.214 / Rpim(I) all: 0.075 / Rrim(I) all: 0.227 / Χ2: 1 / Net I/σ(I): 6.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.56-2.659.14.29449850.2491.4514.5391100
2.65-2.768.92.99949820.4341.0293.1750.999100
2.76-2.888.71.86549740.6420.651.9781100
2.88-3.047.91.13549800.7590.421.2130.99999.6
3.04-3.238.60.64949830.9150.2280.690.99999.9
3.23-3.479.20.37950120.9690.1290.4011100
3.47-3.828.90.21750200.9850.0750.231100
3.82-4.388.10.13550400.990.0490.1440.99999.9
4.38-5.518.40.09650740.9940.0340.1020.99999.8
5.51-508.40.06652490.9980.0230.071.00199.7

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Processing

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

1qub


Resolution: 2.54→47.86 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2332 2003 3.99 %
Rwork0.225 48250 -
obs0.2253 50253 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 186.47 Å2 / Biso mean: 79.1212 Å2 / Biso min: 44.21 Å2
Refinement stepCycle: final / Resolution: 2.54→47.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2530 0 84 0 2614
Biso mean--117.72 --
Num. residues----326
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 (%)
2.54-2.610.42551330.40183206333994
2.61-2.680.41431420.379433963538100
2.68-2.750.36151410.36334873628100
2.76-2.840.30471380.333334053543100
2.84-2.950.31211450.315534183563100
2.95-3.060.32991440.29143439358399
3.06-3.20.29451360.266934413577100
3.2-3.370.2391370.265534413578100
3.37-3.580.2551440.233934503594100
3.58-3.860.24511440.210534743618100
3.86-4.250.2051460.17434693615100
4.25-4.860.15941430.157934773620100
4.86-6.120.17221470.17435273674100
6.12-47.860.22861630.226736203783100
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)
13.6368-2.1272-0.84771.2970.8934.6943-0.1327-0.0504-0.2730.24770.0669-0.03930.61610.188700.6119-0.0244-0.0230.58360.00620.62987.761998.9861135.3282
21.22410.29861.58973.2698-0.26183.3841-0.1277-0.020.11440.0275-0.0152-0.0946-0.28890.118500.58860.1075-0.01890.6314-0.00390.68313.982669.3697114.4627
34.0980.7265-1.23682.51741.07732.74390.18490.5256-0.18290.14980.067-0.15810.33740.190300.76740.27330.0290.8486-0.08650.825120.071245.744686.9252
41.6238-1.4652-0.7521.97530.22410.93380.12090.2464-0.08780.0441-0.39750.2523-0.2185-0.7957-00.84410.23670.04131.0254-0.12020.769841.995431.704265.7078
53.25811.95813.87443.53312.31926.72210.07710.2367-0.08310.17890.0085-0.4943-0.28670.782700.81750.0504-0.00940.79640.01990.801877.058731.820474.3177
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 60 )A1 - 60
2X-RAY DIFFRACTION2chain 'A' and (resid 65 through 118 )A65 - 118
3X-RAY DIFFRACTION3chain 'A' and (resid 123 through 181 )A123 - 181
4X-RAY DIFFRACTION4chain 'A' and (resid 186 through 241 )A186 - 241
5X-RAY DIFFRACTION5chain 'A' and (resid 245 through 326 )A245 - 326

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