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- PDB-4tw0: Crystal Structure of SCARB2 in Acidic Condition (pH4.8) -

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Basic information

Entry
Database: PDB / ID: 4tw0
TitleCrystal Structure of SCARB2 in Acidic Condition (pH4.8)
ComponentsScavenger receptor class B member 2
KeywordsPROTEIN BINDING / lipid binding tunnel
Function / homology
Function and homology information


regulation of glucosylceramide catabolic process / regulation of carbohydrate catabolic process / regulation of endosome organization / aminophospholipid transport / endosome to plasma membrane protein transport / regulation of lysosome organization / protein targeting to lysosome / scavenger receptor activity / phosphatidylcholine binding / cargo receptor activity ...regulation of glucosylceramide catabolic process / regulation of carbohydrate catabolic process / regulation of endosome organization / aminophospholipid transport / endosome to plasma membrane protein transport / regulation of lysosome organization / protein targeting to lysosome / scavenger receptor activity / phosphatidylcholine binding / cargo receptor activity / cholesterol binding / phosphatidylserine binding / lysosomal lumen / receptor-mediated endocytosis / sensory perception of sound / clathrin-coated endocytic vesicle membrane / positive regulation of neuron projection development / transmembrane signaling receptor activity / endocytic vesicle membrane / Cargo recognition for clathrin-mediated endocytosis / virus receptor activity / Clathrin-mediated endocytosis / late endosome membrane / protein-folding chaperone binding / endosome membrane / lysosomal membrane / Golgi membrane / focal adhesion / endoplasmic reticulum membrane / enzyme binding / protein homodimerization activity / extracellular exosome / membrane / plasma membrane / cytoplasm
Similarity search - Function
Lysosome membrane protein II / CD36 family / CD36 family
Similarity search - Domain/homology
Lysosome membrane protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.648 Å
Model detailsThe protein was expressed in 293T cell
AuthorsDang, M.H. / Wang, X.X. / Rao, Z.H.
Funding support China, 1items
OrganizationGrant numberCountry
Institute of Biophysics, Chinese Academy of Science2014CB542800 China
CitationJournal: Protein Cell / Year: 2014
Title: Molecular mechanism of SCARB2-mediated attachment and uncoating of EV71
Authors: Dang, M. / Wang, X. / Wang, Q. / Wang, Y. / Lin, J. / Sun, Y. / Li, X. / Zhang, L. / Lou, Z. / Wang, J. / Rao, Z.
History
DepositionJun 29, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Derived calculations
Revision 1.2Jan 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Source and taxonomy
Category: diffrn_source / entity_src_gen ...diffrn_source / entity_src_gen / pdbx_struct_assembly / pdbx_struct_oper_list / software
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.name
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 / 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_close_contact / 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Nov 8, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / struct_conn
Item: _atom_site.auth_seq_id / _chem_comp.pdbx_synonyms ..._atom_site.auth_seq_id / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nonpoly_scheme.pdb_seq_num / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Scavenger receptor class B member 2
B: Scavenger receptor class B member 2
C: Scavenger receptor class B member 2
D: Scavenger receptor class B member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,73332
Polymers180,4204
Non-polymers14,31328
Water0
1
A: Scavenger receptor class B member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6838
Polymers45,1051
Non-polymers3,5787
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Scavenger receptor class B member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6838
Polymers45,1051
Non-polymers3,5787
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Scavenger receptor class B member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6838
Polymers45,1051
Non-polymers3,5787
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Scavenger receptor class B member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6838
Polymers45,1051
Non-polymers3,5787
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.990, 99.636, 125.853
Angle α, β, γ (deg.)90.000, 90.020, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.999986, 0.003649, -0.003718), (-0.003662, 0.999987, -0.0035), (0.003705, 0.003514, 0.999987)-51.8657, 0.302533, 33.444801
2given(-0.999999, -0.001043, -0.00026), (0.001043, -0.999999, -0.001358), (-0.000259, -0.001359, 0.999999)51.916901, -43.257099, -0.025408
3given(-0.999994, -0.002309, -0.002406), (0.00232, -0.999986, -0.004777), (-0.002395, -0.004783, 0.999986)103.971001, -43.417999, 33.718102

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Scavenger receptor class B member 2 / Lysosome membrane protein 2 / 85 kDa lysosomal membrane sialoglycoprotein / LGP85 / CD36 antigen- ...Lysosome membrane protein 2 / 85 kDa lysosomal membrane sialoglycoprotein / LGP85 / CD36 antigen-like 2 / Lysosome membrane protein II / LIMP II


Mass: 45104.969 Da / Num. of mol.: 4 / Fragment: ectodomain, UNP residues 37-429
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCARB2, CD36L2, LIMP2, LIMPII / Plasmid: pFastBac_Bee
Details (production host): modified from pFastBac-one and can express recombinant protein with a melittin tag at the N-terminus and a 6x his-tag at the C-terminus
Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q14108

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Sugars , 5 types, 28 molecules

#2: Polysaccharide
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 4 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 951.875 Da / Num. of mol.: 4 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-1/a4-b1_b4-c1_c3-d1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}}}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.: 8 / Source method: obtained synthetically
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
#5: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-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.: 4 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_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
#6: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8 / 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

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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: 3.61 Å3/Da / Density % sol: 65.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 mol/L ammonium sulfate, 0.1 mol/L sodium acetate trihydrate(pH 4.8), 30% w/v polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.91998 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91998 Å / Relative weight: 1
ReflectionResolution: 3.648→50 Å / Num. obs: 28909 / % possible obs: 98.4 % / Redundancy: 2.9 % / Biso Wilson estimate: 62.61 Å2 / Rmerge(I) obs: 0.141 / Net I/σ(I): 6.5
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.65-3.712.90.70714081.40498.1
3.71-3.7830.76314331.27999.1
3.78-3.852.90.65114481.25498.1
3.85-3.932.90.51814481.40397.9
3.93-4.022.90.54414101.21598
4.02-4.112.90.41614291.16998.8
4.11-4.2130.35214581.17798.3
4.21-4.332.90.28814361.11898.8
4.33-4.4530.21314521.16699
4.45-4.630.22514331.13498.5
4.6-4.762.90.1714341.08898.6
4.76-4.9530.13914411.05598.5
4.95-5.1830.12514721.03798.9
5.18-5.4530.15314381.03198.8
5.45-5.792.90.14814521.08698.7
5.79-6.242.90.11514601.11298.8
6.24-6.8630.09114471.11897.9
6.86-7.852.90.07214651.08598.7
7.85-9.882.90.04914651.03397.9
9.88-502.80.0414800.98996.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
SCALEPACKdata reduction
PHASERphasing
PDB_EXTRACT3.14data extraction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F7B

4f7b


Resolution: 3.648→48.06 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3035 1166 5.06 %Random selection
Rwork0.2492 21869 --
obs0.2519 23035 79.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 174.69 Å2 / Biso mean: 60.2779 Å2 / Biso min: 15.17 Å2
Refinement stepCycle: final / Resolution: 3.648→48.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12187 0 948 0 13135
Biso mean--88.61 --
Num. residues----1571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613539
X-RAY DIFFRACTIONf_angle_d1.28118592
X-RAY DIFFRACTIONf_chiral_restr0.0692280
X-RAY DIFFRACTIONf_plane_restr0.0052294
X-RAY DIFFRACTIONf_dihedral_angle_d14.4744751
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.6481-3.81410.4133500.345592097027
3.8141-4.01510.36780.32391783186152
4.0151-4.26650.32181310.27242523265474
4.2665-4.59570.31061580.25573211336994
4.5957-5.05770.2742090.22533328353799
5.0577-5.78850.27161650.24543416358199
5.7885-7.28890.31531850.24673362354798
7.2889-48.06450.29861900.21883326351695

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