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- PDB-6k0l: The crystal structure of simian CD163 SRCR5 -

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Basic information

Entry
Database: PDB / ID: 6k0l
TitleThe crystal structure of simian CD163 SRCR5
ComponentsScavenger receptor cysteine-rich type 1 protein M130
KeywordsENDOCYTOSIS / Scavenger receptor / Scavenger receptor cysteine-rich domain / Porcine reproductive and respiratory syndrome virus
Function / homology
Function and homology information


scavenger receptor activity / acute-phase response / membrane => GO:0016020 / extracellular region / plasma membrane
Similarity search - Function
Mac-2 Binding Protein / SRCR-like domain / SRCR domain signature. / Scavenger receptor cysteine-rich domain / SRCR domain / SRCR domain profile. / SRCR-like domain / SRCR-like domain superfamily / Scavenger receptor Cys-rich / Roll / Alpha Beta
Similarity search - Domain/homology
Scavenger receptor cysteine-rich type 1 protein M130
Similarity search - Component
Biological speciesChlorocebus aethiops (grivet)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsMa, H. / Li, R. / Jiang, L. / Qiao, S. / Zhang, G.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31490601 China
National Natural Science Foundation of China31602036 China
CitationJournal: Vet Res / Year: 2021
Title: Structural comparison of CD163 SRCR5 from different species sheds some light on its involvement in porcine reproductive and respiratory syndrome virus-2 infection in vitro.
Authors: Ma, H. / Li, R. / Jiang, L. / Qiao, S. / Chen, X.X. / Wang, A. / Zhang, G.
History
DepositionMay 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 24, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 22, 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: Scavenger receptor cysteine-rich type 1 protein M130
B: Scavenger receptor cysteine-rich type 1 protein M130


Theoretical massNumber of molelcules
Total (without water)22,7892
Polymers22,7892
Non-polymers00
Water3,945219
1
A: Scavenger receptor cysteine-rich type 1 protein M130


Theoretical massNumber of molelcules
Total (without water)11,3951
Polymers11,3951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Scavenger receptor cysteine-rich type 1 protein M130


Theoretical massNumber of molelcules
Total (without water)11,3951
Polymers11,3951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.623, 33.465, 46.726
Angle α, β, γ (deg.)71.02, 75.29, 84.91
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 11394.694 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorocebus aethiops (grivet) / Gene: CD163, M130 / Production host: Komagataella pastoris (fungus) / References: UniProt: Q2VLG4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O

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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: 1.81 Å3/Da / Density % sol: 31.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Bis-Tris pH5.5, 25% PEG 3350, 0.2M NaCl

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 20604 / % possible obs: 95.1 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 24.6
Reflection shellResolution: 1.58→1.64 Å / Rmerge(I) obs: 0.096 / Num. unique obs: 2039

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
xia2data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BY2

1by2


Resolution: 1.58→31.66 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.412 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.193 1063 5.2 %RANDOM
Rwork0.158 ---
obs0.16 19537 94.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å2-0.03 Å2-0.01 Å2
2---0.02 Å20.06 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.58→31.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1578 0 0 219 1797
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0141616
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171378
X-RAY DIFFRACTIONr_angle_refined_deg1.1691.6432189
X-RAY DIFFRACTIONr_angle_other_deg0.9371.6413250
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4515209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.16421.80783
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.18315251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9741512
X-RAY DIFFRACTIONr_chiral_restr0.0550.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021853
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02287
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_it1.0941.239848
X-RAY DIFFRACTIONr_mcbond_other1.0921.238847
X-RAY DIFFRACTIONr_mcangle_it1.851.8541053
X-RAY DIFFRACTIONr_mcangle_other1.851.8551054
X-RAY DIFFRACTIONr_scbond_it1.5841.428768
X-RAY DIFFRACTIONr_scbond_other1.5831.426766
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4562.0791136
X-RAY DIFFRACTIONr_long_range_B_refined5.23516.9981865
X-RAY DIFFRACTIONr_long_range_B_other4.96916.1671804
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.58→1.62 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.198 83 -
Rwork0.156 1343 -
obs--90.31 %

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