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- PDB-8h7j: The crystal structure of CD163 SRCR5-9 -

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Basic information

Entry
Database: PDB / ID: 8h7j
TitleThe crystal structure of CD163 SRCR5-9
ComponentsScavenger receptor cysteine-rich type 1 protein M130
KeywordsENDOCYTOSIS / CD163 / arterivirus receptor / SRCR / long-range SRCR repeat / putative arterivirus interaction domains
Function / homology
Function and homology information


acute-phase response / virus receptor activity / external side of plasma membrane / extracellular region
Similarity search - Function
: / SRCR domain signature. / Scavenger receptor cysteine-rich domain / SRCR domain / SRCR domain profile. / SRCR-like domain / SRCR-like domain superfamily / Scavenger receptor Cys-rich
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: 2.5 Å
AuthorsLuo, Z.P. / Li, R. / Ma, H.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: The crystal structure of CD163 SRCR5-9
Authors: Ma, H.F. / Li, R. / Luo, Z.P.
History
DepositionOct 20, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)62,8646
Polymers60,5161
Non-polymers2,3485
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.328, 60.085, 85.424
Angle α, β, γ (deg.)90.000, 114.120, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 60516.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: CD163, M130 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q2VL90
#2: 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.: 2
Source method: isolated from a genetically manipulated source
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
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-2-2-3/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: 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.: 2 / 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.46 Å3/Da / Density % sol: 50.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG 4000, 0.15M potassium sodium tartrate tetra-hydrate pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 20350 / % possible obs: 98.7 % / Redundancy: 6.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.059 / Net I/σ(I): 21.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.552 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1962 / CC1/2: 0.761 / Rpim(I) all: 0.779 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JFB

5jfb


Resolution: 2.5→48.487 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.922 / SU B: 8.676 / SU ML: 0.197 / Cross valid method: FREE R-VALUE / ESU R: 1.026 / ESU R Free: 0.268
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2123 936 4.811 %
Rwork0.1822 18519 -
all0.184 --
obs-19455 94.031 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 59.455 Å2
Baniso -1Baniso -2Baniso -3
1--0.066 Å2-0 Å20.067 Å2
2---0.411 Å20 Å2
3---0.297 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4130 0 156 111 4397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0124415
X-RAY DIFFRACTIONr_bond_other_d0.0090.0163670
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.6486004
X-RAY DIFFRACTIONr_angle_other_deg0.5521.578612
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6835554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.186527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88910640
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.66910188
X-RAY DIFFRACTIONr_chiral_restr0.0630.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.025083
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02858
X-RAY DIFFRACTIONr_nbd_refined0.1460.2583
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.23283
X-RAY DIFFRACTIONr_nbtor_refined0.1610.22148
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.10.22203
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2123
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0410.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1940.218
X-RAY DIFFRACTIONr_nbd_other0.1690.262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1760.29
X-RAY DIFFRACTIONr_mcbond_it9.90811.9612219
X-RAY DIFFRACTIONr_mcbond_other9.88511.962219
X-RAY DIFFRACTIONr_mcangle_it12.18522.3922772
X-RAY DIFFRACTIONr_mcangle_other12.18422.3962773
X-RAY DIFFRACTIONr_scbond_it12.50213.6342196
X-RAY DIFFRACTIONr_scbond_other12.49913.6372197
X-RAY DIFFRACTIONr_scangle_it15.44724.8033232
X-RAY DIFFRACTIONr_scangle_other15.44424.8063233
X-RAY DIFFRACTIONr_lrange_it16.699120.51317963
X-RAY DIFFRACTIONr_lrange_other16.707120.5617930
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.5610.287460.221911X-RAY DIFFRACTION64.1421
2.561-2.6310.227610.2151167X-RAY DIFFRACTION82.638
2.631-2.7070.26620.2071229X-RAY DIFFRACTION89.4664
2.707-2.790.263630.2011248X-RAY DIFFRACTION95.0689
2.79-2.8820.21590.1821275X-RAY DIFFRACTION98.0882
2.882-2.9820.263640.1811226X-RAY DIFFRACTION98.9264
2.982-3.0950.247510.1871193X-RAY DIFFRACTION98.8871
3.095-3.220.221690.1721143X-RAY DIFFRACTION97.8998
3.22-3.3630.253520.181085X-RAY DIFFRACTION96.6837
3.363-3.5260.164590.1671048X-RAY DIFFRACTION99.5504
3.526-3.7160.17520.1651021X-RAY DIFFRACTION99.6286
3.716-3.940.207480.16947X-RAY DIFFRACTION99.2024
3.94-4.210.17500.155896X-RAY DIFFRACTION99.1614
4.21-4.5440.154430.156827X-RAY DIFFRACTION98.3051
4.544-4.9740.18330.152771X-RAY DIFFRACTION96.6346
4.974-5.5530.211310.184714X-RAY DIFFRACTION99.866
5.553-6.3980.297360.228624X-RAY DIFFRACTION100
6.398-7.8030.214230.206531X-RAY DIFFRACTION98.227

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