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- PDB-1by2: STRUCTURE OF M2BP SCAVENGER RECEPTOR CYSTEINE-RICH DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1by2
TitleSTRUCTURE OF M2BP SCAVENGER RECEPTOR CYSTEINE-RICH DOMAIN
ComponentsMAC-2 BINDING PROTEIN
KeywordsEXTRACELLULAR MODULE / SCAVENGER RECEPTOR / TUMOUR-ASSOCIATED ANTIGEN / EXTRACELLULAR MATRIX / GLYCOSYLATED PROTEIN
Function / homology
Function and homology information


platelet dense granule lumen / scavenger receptor activity / cellular defense response / Platelet degranulation / : / blood microparticle / cell adhesion / signal transduction / extracellular space / extracellular exosome ...platelet dense granule lumen / scavenger receptor activity / cellular defense response / Platelet degranulation / : / blood microparticle / cell adhesion / signal transduction / extracellular space / extracellular exosome / extracellular region / membrane
Similarity search - Function
: / Mac-2 Binding Protein / SRCR-like domain / SRCR domain signature. / Scavenger receptor cysteine-rich domain / SRCR domain profile. / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SRCR domain / BTB/Kelch-associated ...: / Mac-2 Binding Protein / SRCR-like domain / SRCR domain signature. / Scavenger receptor cysteine-rich domain / SRCR domain profile. / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SRCR domain / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / BTB domain profile. / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Galectin-3-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2 Å
AuthorsHohenester, E. / Sasaki, T. / Timpl, R.
Citation
Journal: Nat.Struct.Biol. / Year: 1999
Title: Crystal structure of a scavenger receptor cysteine-rich domain sheds light on an ancient superfamily.
Authors: Hohenester, E. / Sasaki, T. / Timpl, R.
#1: Journal: Embo J. / Year: 1998
Title: Mac-2 Binding Protein is a Cell-Adhesive Protein of the Extracellular Matrix which Self-Assembles Into Ring-Like Structures and Binds Beta1 Integrins, Collagens and Fibronectin
Authors: Sasaki, T. / Brakebusch, C. / Engel, J. / Timpl, R.
#2: Journal: Trends Biochem.Sci. / Year: 1994
Title: The Srcr Superfamily: A Family Reminiscent of the Ig Superfamily
Authors: Resnick, D. / Pearson, A. / Krieger, M.
History
DepositionOct 23, 1998Processing site: BNL
Revision 1.0May 18, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MAC-2 BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9262
Polymers12,7051
Non-polymers2211
Water1,02757
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.630, 44.630, 134.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein MAC-2 BINDING PROTEIN / TUMOR-ASSOCIATED ANTIGEN 90K


Mass: 12705.093 Da / Num. of mol.: 1 / Fragment: SCAVENGER RECEPTOR CYSTEINE-RICH (SRCR) DOMAIN / Mutation: N-TERMINAL APLA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: 293-EBNA / Organ: KIDNEY / Cell line (production host): 293-EBNA / Production host: Homo sapiens (human) / References: UniProt: Q08380
#2: 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.: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
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

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 50 %
Description: TWO DERIVATIVES (SMCL3 AND UO2SO4) WERE USED AT 3.0 A
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
210 mMTris1drop
350 mMBis-Tris1reservoir
430-32 %PEG15001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 7, 1998
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 9843 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 7.3
Reflection shellResolution: 2→2.11 Å / Redundancy: 6 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 3.7 / % possible all: 100
Reflection
*PLUS
Num. measured all: 60557

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA(CCP4)data scaling
CCP4model building
X-PLOR3.84refinement
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: MIRAS / Resolution: 2→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0
Isotropic thermal model: INDIVIDUAL RESTRAINED, RMS BONDS 3.5 A**2
Cross valid method: FREE R-FACTOR / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.218 934 10 %RANDOM
Rwork0.186 ---
obs0.186 9649 99.6 %-
Displacement parametersBiso mean: 20 Å2
Refine analyzeLuzzati d res low obs: 6 Å / Luzzati sigma a obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms832 0 14 57 903
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it4
LS refinement shellResolution: 2→2.09 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.277 114 10 %
Rwork0.27 1056 -
obs--100 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WAT
X-RAY DIFFRACTION3PARAM3_MOD.CHO
Software
*PLUS
Name: X-PLOR / Version: 3.84 / Classification: refinement
LS refinement shell
*PLUS
Rfactor Rwork: 0.27

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