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- PDB-6k0o: The crystal structure of human CD163-like homolog SRCR8 -

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Basic information

Entry
Database: PDB / ID: 6k0o
TitleThe crystal structure of human CD163-like homolog SRCR8
ComponentsScavenger receptor cysteine-rich type 1 protein M160
KeywordsENDOCYTOSIS / Scavenger receptor / Scavenger receptor cysteine-rich domain / Porcine reproductive and respiratory syndrome virus
Function / homology
Function and homology information


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 / SRCR domain profile. / SRCR-like domain / SRCR-like domain superfamily / Scavenger receptor Cys-rich ...: / 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 M160
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsMa, H. / Li, R. / Jiang, L. / Qiao, S. / Zhang, G.
Funding support2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31490601
National Natural Science Foundation of China31602036
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 / Refinement description
Category: citation / citation_author ...citation / citation_author / database_2 / refine_hist
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 / _refine_hist.d_res_low
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 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 M160
B: Scavenger receptor cysteine-rich type 1 protein M160


Theoretical massNumber of molelcules
Total (without water)22,5352
Polymers22,5352
Non-polymers00
Water1,71195
1
A: Scavenger receptor cysteine-rich type 1 protein M160


Theoretical massNumber of molelcules
Total (without water)11,2681
Polymers11,2681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Scavenger receptor cysteine-rich type 1 protein M160


Theoretical massNumber of molelcules
Total (without water)11,2681
Polymers11,2681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.497, 73.043, 82.740
Angle α, β, γ (deg.)90.00, 89.96, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-940-

HOH

21B-941-

HOH

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Components

#1: Protein Scavenger receptor cysteine-rich type 1 protein M160 / CD163 antigen-like 1


Mass: 11267.665 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD163L1, CD163B, M160, UNQ6434/PRO23202 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q9NR16
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 1.98 Å3/Da / Density % sol: 37.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M citric acid pH3.5, 15% PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / 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: 2→50 Å / Num. obs: 11711 / % possible obs: 98.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.152 / Net I/σ(I): 13.4
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.378 / Num. unique obs: 557

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
xia2data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JFB

5jfb


Resolution: 1.99→41.37 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.894 / SU B: 13.306 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26904 568 4.9 %RANDOM
Rwork0.19495 ---
obs0.19856 11071 96.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.794 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å2-0.1 Å2
2--0.14 Å20 Å2
3---0.45 Å2
Refinement stepCycle: 1 / Resolution: 1.99→41.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1566 0 0 95 1661
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191604
X-RAY DIFFRACTIONr_bond_other_d0.0030.021416
X-RAY DIFFRACTIONr_angle_refined_deg1.6421.9252174
X-RAY DIFFRACTIONr_angle_other_deg0.9733292
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7095204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.08223.61172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.30415254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7591512
X-RAY DIFFRACTIONr_chiral_restr0.1060.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021800
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02324
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_it2.2622.375828
X-RAY DIFFRACTIONr_mcbond_other2.2622.374827
X-RAY DIFFRACTIONr_mcangle_it2.7883.5461028
X-RAY DIFFRACTIONr_mcangle_other2.7883.5481029
X-RAY DIFFRACTIONr_scbond_it2.8452.778776
X-RAY DIFFRACTIONr_scbond_other2.8442.78777
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3384.0461147
X-RAY DIFFRACTIONr_long_range_B_refined4.0931.6851953
X-RAY DIFFRACTIONr_long_range_B_other4.01231.6311947
X-RAY DIFFRACTIONr_rigid_bond_restr8.52733020
X-RAY DIFFRACTIONr_sphericity_free29.056541
X-RAY DIFFRACTIONr_sphericity_bonded6.97753036
LS refinement shellResolution: 1.992→2.044 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 30 -
Rwork0.21 589 -
obs--70.42 %

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