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- PDB-7kg4: Recombinant Beta-2-Glycoprotein I antibody recognition loop mutant -

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Basic information

Entry
Database: PDB / ID: 7kg4
TitleRecombinant Beta-2-Glycoprotein I antibody recognition loop mutant
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 / blood coagulation, intrinsic pathway / chylomicron / negative regulation of myeloid cell apoptotic process / regulation of fibrinolysis / very-low-density lipoprotein particle / high-density lipoprotein particle ...lipoprotein lipase activator activity / triglyceride transport / platelet dense granule lumen / positive regulation of lipoprotein lipase activity / blood coagulation, intrinsic pathway / chylomicron / negative regulation of myeloid cell apoptotic process / regulation of fibrinolysis / very-low-density lipoprotein particle / high-density lipoprotein particle / negative regulation of blood coagulation / triglyceride metabolic process / negative regulation of endothelial cell migration / 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
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: 3.3 Å
AuthorsKlenotic, P.A. / Yu, E.W.
CitationJournal: To be published
Title: Beta-2-Glycoprotein I and its role in APS
Authors: Klenotic, P.A. / Yu, E.W.
History
DepositionOct 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-2-glycoprotein 1
B: Beta-2-glycoprotein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4639
Polymers72,3392
Non-polymers3,1247
Water00
1
A: Beta-2-glycoprotein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9155
Polymers36,1691
Non-polymers1,7464
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-2-glycoprotein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5484
Polymers36,1691
Non-polymers1,3783
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.209, 114.694, 124.293
Angle α, β, γ (deg.)90.000, 96.920, 90.000
Int Tables number4
Space group name H-MP1211

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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: 36169.332 Da / Num. of mol.: 2 / Mutation: R39S, G40E, M42V, R43G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOH, B2G1 / 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.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-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: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: 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.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / 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 / pH: 7.5
Details: 100mM HEPES, pH 7.5, 1.8M Ammonium Sulfate, 20mM Calcium Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.29→50 Å / Num. obs: 47077 / % possible obs: 97.3 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.313 / Rpim(I) all: 0.163 / Rrim(I) all: 0.354 / Χ2: 1.086 / Net I/σ(I): 4.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.3-3.364.42.4822100.1511.2592.7930.88291.8
3.36-3.424.41.80322410.2510.9162.0320.91194.1
3.42-3.484.41.66622700.2790.8441.8770.93294
3.48-3.554.41.30323000.4660.6611.4680.93995.4
3.55-3.634.41.07922970.5580.5511.2180.92996.4
3.63-3.724.31.00523310.6360.521.1370.96897
3.72-3.814.20.76323780.7170.3990.8660.94298.2
3.81-3.914.20.66723500.7470.3520.7591.06398.6
3.91-4.034.20.53624160.8390.2850.6110.98999.1
4.03-4.164.30.39623730.9170.2090.451.01798.5
4.16-4.314.30.36323660.9060.1940.4131.07198.4
4.31-4.484.30.29623530.9220.1590.3381.11697.9
4.48-4.6840.26223300.9440.1460.3021.11496.6
4.68-4.9340.21923400.960.1220.2531.11296
4.93-5.244.80.18124200.9810.0920.2041.11799.7
5.24-5.644.90.17423980.9760.0870.1951.13499.3
5.64-6.214.80.15324140.9850.0760.1711.299.5
6.21-7.14.70.12524280.9870.0640.1411.28399.6
7.1-8.944.30.08224020.9910.0440.0931.38497.8
8.94-504.40.05424600.9960.0280.0611.50798.4

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Processing

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

1qub


Resolution: 3.3→49.99 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.298 1985 4.23 %
Rwork0.2831 44988 -
obs0.2838 46973 95.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 200.36 Å2 / Biso mean: 91.3369 Å2 / Biso min: 28.25 Å2
Refinement stepCycle: final / Resolution: 3.3→49.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5062 0 206 0 5268
Biso mean--128.49 --
Num. residues----652
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 (%)
3.29-3.380.419970.39172222231966
3.38-3.470.39521320.36053161329394
3.47-3.570.32471450.34223180332595
3.57-3.680.30931500.33783229337996
3.68-3.820.32621370.32053275341298
3.82-3.970.30751540.31033301345599
3.97-4.150.31941400.27993339347999
4.15-4.370.33371550.27383277343298
4.37-4.640.29711410.25953284342597
4.64-50.30781440.2533255339996
5-5.50.23011470.24233339348699
5.5-6.30.26591470.26893366351399
6.3-7.930.28121490.27013374352399
7.93-49.990.27081470.26453386353398
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)
12.2266-1.3789-1.2660.51720.99791.4983-0.1548-0.1918-0.14390.13740.1260.28770.30970.05890.0250.411-0.06290.05550.41540.03520.4949162.4414-123.437253.5759
20.8967-1.5620.26990.8251-1.2497-0.7515-0.4180.14060.7015-0.26050.1872-0.71180.17160.1223-0.05240.02580.2912-0.06750.6745-0.15021.197999.0869-75.30860.1473
30.19440.13440.10320.09260.0580.0590.4694-0.1537-0.0105-0.7271-0.86650.54110.5392-0.84110.00151.3339-0.12760.03320.9427-0.27711.841259.5937-67.486435.5546
41.06781.27760.5773.227-2.12055.1926-0.3641-0.23880.0101-0.6876-0.0721-0.2874-0.2958-0.44120.06190.6533-0.001-0.23740.64880.35840.674267.4211-77.89931.9836
50.12340.35710.08043.5824-0.69031.4062-0.2557-0.0595-0.12730.65340.0352-0.2243-0.2294-0.11560.0960.40150.0172-0.07280.37-0.03070.4364184.0143-33.430356.1599
61.07450.6251-0.68922.2917-1.11060.81860.0246-0.0364-00.09830.0644-0.13560.2641-0.2354-0.15050.7302-0.00770.01680.5494-0.02070.2549157.9258-59.234385.7413
7-0.2596-0.1951-0.1415-0.1704-0.64770.0381-0.0851-0.08140.4339-0.77040.30490.17420.9959-0.71030.04551.735-0.45-0.2070.93820.37360.2408148.2386-91.7862128.678
83.28881.0590.90022.30510.30442.05620.12140.3477-0.2090.00680.3024-0.70740.24970.0119-0.30741.03090.040.00610.5908-0.02740.5254168.0194-94.0441159.7952
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 116 )A1 - 116
2X-RAY DIFFRACTION2chain 'A' and (resid 117 through 307 )A117 - 307
3X-RAY DIFFRACTION3chain 'A' and (resid 308 through 316 )A308 - 316
4X-RAY DIFFRACTION4chain 'A' and (resid 317 through 326 )A317 - 326
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 58 )B1 - 58
6X-RAY DIFFRACTION6chain 'B' and (resid 59 through 149 )B59 - 149
7X-RAY DIFFRACTION7chain 'B' and (resid 150 through 266 )B150 - 266
8X-RAY DIFFRACTION8chain 'B' and (resid 267 through 326 )B267 - 326

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