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- PDB-1c1z: CRYSTAL STRUCTURE OF HUMAN BETA-2-GLYCOPROTEIN-I (APOLIPOPROTEIN-H) -

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Basic information

Entry
Database: PDB / ID: 1c1z
TitleCRYSTAL STRUCTURE OF HUMAN BETA-2-GLYCOPROTEIN-I (APOLIPOPROTEIN-H)
ComponentsBETA2-GLYCOPROTEIN-I
KeywordsSIGNALING PROTEIN / GLYCOPROTEIN / SHORT CONSENSUS REPEAT / SCR / SUSHI DOMAIN / COMPLEMENT CONTROL PROTEIN MODULE / CCP
Function / homology
Function and homology information


lipoprotein lipase activator activity / triglyceride transport / platelet dense granule lumen / chylomicron / positive regulation of lipoprotein lipase activity / blood coagulation, intrinsic pathway / very-low-density lipoprotein particle / negative regulation of smooth muscle cell apoptotic process / negative regulation of blood coagulation / high-density lipoprotein particle ...lipoprotein lipase activator activity / triglyceride transport / platelet dense granule lumen / chylomicron / positive regulation of lipoprotein lipase activity / blood coagulation, intrinsic pathway / very-low-density lipoprotein particle / negative regulation of smooth muscle cell apoptotic process / negative regulation of blood coagulation / high-density lipoprotein particle / negative regulation of myeloid cell apoptotic process / regulation of fibrinolysis / negative regulation of endothelial cell migration / triglyceride metabolic process / plasminogen activation / negative regulation of endothelial cell proliferation / 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 / Complement Module, domain 1 / Complement Module; domain 1 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/SCR/CCP superfamily / Sushi/CCP/SCR domain profile. / Ribbon / Mainly Beta
Similarity search - Domain/homology
: / Beta-2-glycoprotein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR-MAD COMBINATION / Resolution: 2.87 Å
AuthorsSchwarzenbacher, R. / Zeth, K. / Diederichs, K. / Gries, A. / Kostner, G.M. / Laggner, P. / Prassl, R.
Citation
Journal: EMBO J. / Year: 1999
Title: Crystal structure of human beta2-glycoprotein I: implications for phospholipid binding and the antiphospholipid syndrome.
Authors: Schwarzenbacher, R. / Zeth, K. / Diederichs, K. / Gries, A. / Kostner, G.M. / Laggner, P. / Prassl, R.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallization and preliminary X-ray crystallographic studies on apolipoprotein H (beta-2-glycoprotein-I)
Authors: Saxena, A. / Gries, A. / Schwarzenbacher, R. / Kostner, G.M. / Laggner, P. / Prassl, R.
History
DepositionJul 22, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / diffrn_source / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA2-GLYCOPROTEIN-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4575
Polymers36,3141
Non-polymers2,1434
Water39622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)159.500, 164.800, 114.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein / Non-polymers , 2 types, 23 molecules A

#1: Protein BETA2-GLYCOPROTEIN-I


Mass: 36313.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: BLOOD / References: GenBank: 28810, UniProt: P02749*PLUS
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 4 types, 4 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAca1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3[DManpa1-6]DManpb1-4DGlcpNAca1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-3-3-4/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}[(6+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 8.86 Å3/Da / Density % sol: 84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: Ammonium sulfate, phosphate buffer, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, sitting drop
Details: Saxena, A., (1998) Acta Crystallogr., Sect.D, 54, 1450.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
21.6-2.0 Mammonium sulfate1reservoir
30.2 %sodium carbonate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.95
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 25, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.87→50 Å / Num. obs: 32406 / % possible obs: 93.2 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 37.9 Å2 / Rmerge(I) obs: 0.086
Reflection shellResolution: 2.87→3.05 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.43 / % possible all: 60.1
Reflection
*PLUS
Highest resolution: 2.87 Å / Lowest resolution: 50 Å / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Num. measured all: 103699 / Biso Wilson estimate: 37.9 Å2
Reflection shell
*PLUS
% possible obs: 60.1 % / Redundancy: 2.1 % / Mean I/σ(I) obs: 2.7

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Processing

Software
NameClassification
XDSdata scaling
XDSdata reduction
SHARPphasing
CNSrefinement
RefinementMethod to determine structure: MIR-MAD COMBINATION / Resolution: 2.87→50 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: SIMULATED ANNEALING REFINEMENT WITH MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES, TORSION ANGLE DYNAMICS, BULK SOLVENT CORRECTION, ANISOTROPIC B- FACTOR CORRECTION AND GROUPED B-FACTOR ...Details: SIMULATED ANNEALING REFINEMENT WITH MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES, TORSION ANGLE DYNAMICS, BULK SOLVENT CORRECTION, ANISOTROPIC B- FACTOR CORRECTION AND GROUPED B-FACTOR REFINEMENT SIDE CHAIN POSITIONS OF RESIDUES ARG2, ARG39, LYS59, LYS110, ARG135, GLN158, LYS177, LYS208, LYS251, LYS284, GLU285, LYS286, LYS287, LYS308, LEU313 AND PHE315 ARE POORLY DEFINED
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1608 5 %RANDOM
Rwork0.238 ---
obs0.238 32406 93.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.03 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso mean: 55.3 Å2
Baniso -1Baniso -2Baniso -3
1--7.117 Å20 Å20 Å2
2---3.122 Å20 Å2
3---10.239 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.43 Å
Luzzati d res low-8 Å
Luzzati sigma a0.97 Å0.8 Å
Refinement stepCycle: LAST / Resolution: 2.87→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2541 0 142 22 2705
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.57
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.87→3.05 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.392 -5 %
Rwork0.368 3286 -
obs--60.1 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.57
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92
LS refinement shell
*PLUS
Rfactor Rfree: 0.392 / % reflection Rfree: 5 % / Rfactor Rwork: 0.368

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