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- PDB-5jfb: Crystal structure of the scavenger receptor cysteine-rich domain ... -

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Basic information

Entry
Database: PDB / ID: 5jfb
TitleCrystal structure of the scavenger receptor cysteine-rich domain 5 (SRCR5) from porcine CD163
ComponentsScavenger receptor cysteine-rich type 1 protein M130
KeywordsENDOCYTOSIS / CD163 / SRCR / PRRSV
Function / homology
Function and homology information


acute-phase response / virus receptor activity / external side of plasma membrane / extracellular region
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 / Roll / Alpha Beta
Similarity search - Domain/homology
Scavenger receptor cysteine-rich type 1 protein M130
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMa, H. / Jiang, L. / Qiao, S. / Zhang, G. / Li, R.
CitationJournal: J. Virol. / Year: 2017
Title: The Crystal Structure of the Fifth Scavenger Receptor Cysteine-Rich Domain of Porcine CD163 Reveals an Important Residue Involved in Porcine Reproductive and Respiratory Syndrome Virus Infection
Authors: Ma, H. / Jiang, L. / Qiao, S. / Zhi, Y. / Chen, X.X. / Yang, Y. / Huang, X. / Huang, M. / Li, R. / Zhang, G.P.
History
DepositionApr 19, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Scavenger receptor cysteine-rich type 1 protein M130


Theoretical massNumber of molelcules
Total (without water)12,0831
Polymers12,0831
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.711, 73.930, 87.527
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Scavenger receptor cysteine-rich type 1 protein M130


Mass: 12083.336 Da / Num. of mol.: 1 / Fragment: SRCR 5 domain, UNP residues 477-577
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: CD163, M130 / Plasmid: pMT/BiP/Blast / Cell line (production host): SCHNEIDER'S S2 / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: Q2VL90
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 1.99 Å3/Da / Density % sol: 38.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 25% (w/v) PEG 4000, 200mM (NH4)2SO4 in 100mM sodium acetate at pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: Pilatus / Detector: CMOS / Date: Sep 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 6682 / % possible obs: 97.1 % / Redundancy: 10 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 17.7
Reflection shellResolution: 2→2.07 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-3000data processing
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BY2

1by2


Resolution: 2→43.76 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.562 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23905 319 4.9 %RANDOM
Rwork0.20767 ---
obs0.20922 6223 95.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å2-0 Å2
2--0.16 Å2-0 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2→43.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms761 0 0 41 802
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.019779
X-RAY DIFFRACTIONr_bond_other_d0.0020.02692
X-RAY DIFFRACTIONr_angle_refined_deg1.2761.9341056
X-RAY DIFFRACTIONr_angle_other_deg0.9231600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3375101
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.55423.52934
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13915114
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.415156
X-RAY DIFFRACTIONr_chiral_restr0.0710.2116
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021892
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02176
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0462.279413
X-RAY DIFFRACTIONr_mcbond_other1.0472.278412
X-RAY DIFFRACTIONr_mcangle_it1.7443.39511
X-RAY DIFFRACTIONr_mcangle_other1.7433.391512
X-RAY DIFFRACTIONr_scbond_it1.3912.415366
X-RAY DIFFRACTIONr_scbond_other1.3832.415366
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2423.583546
X-RAY DIFFRACTIONr_long_range_B_refined4.21218.223834
X-RAY DIFFRACTIONr_long_range_B_other4.17518.188830
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.996→2.048 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 13 -
Rwork0.198 385 -
obs--83.44 %

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