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- PDB-8te5: Crystal structure of a multiple lysine-to-arginine substitution m... -

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Basic information

Entry
Database: PDB / ID: 8te5
TitleCrystal structure of a multiple lysine-to-arginine substitution mutant of the human CRIg C3b-binding domain
ComponentsV-set and immunoglobulin domain-containing protein 4
KeywordsIMMUNE SYSTEM / receptor / complement / C3b-binding
Function / homology
Function and homology information


negative regulation of complement activation, alternative pathway / negative regulation of macrophage activation / complement component C3b binding / complement activation, alternative pathway / negative regulation of interleukin-2 production / negative regulation of T cell proliferation / protein-containing complex / membrane
Similarity search - Function
VSIG4, immunoglobulin variable (IgV)-like domain / V-set and immunoglobulin domain-containing protein 4 / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin ...VSIG4, immunoglobulin variable (IgV)-like domain / V-set and immunoglobulin domain-containing protein 4 / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
V-set and immunoglobulin domain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.502 Å
AuthorsAbram, T.G. / Geisbrecht, B.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM140852 United States
CitationJournal: Immunohorizons / Year: 2023
Title: New Insights into the Complement Receptor of the Ig Superfamily Obtained from Structural and Functional Studies on Two Mutants.
Authors: Duan, H. / Abram, T.G. / Cruz, A.R. / Rooijakkers, S.H.M. / Geisbrecht, B.V.
History
DepositionJul 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: V-set and immunoglobulin domain-containing protein 4


Theoretical massNumber of molelcules
Total (without water)13,9441
Polymers13,9441
Non-polymers00
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.006, 49.776, 60.029
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein V-set and immunoglobulin domain-containing protein 4 / Protein Z39Ig


Mass: 13944.488 Da / Num. of mol.: 1 / Mutation: K15R,K36R,K62R,K72R,K110R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VSIG4, CRIg, Z39IG, UNQ317/PRO362 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y279
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 1.66 Å3/Da / Density % sol: 25.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium aaetate (pH 6.5) 0.2 M ammonium acetate 30% (w/v) peg-4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 15185 / % possible obs: 99.1 % / Redundancy: 7 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.061 / Rrim(I) all: 0.165 / Χ2: 0.99 / Net I/σ(I): 10.1 / Num. measured all: 105683
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.5-1.555.40.80114840.7020.9080.3760.8880.96699.5
1.55-1.626.20.89714960.6440.8850.3940.9831.02899.7
1.62-1.696.90.91714890.5610.8480.3860.9991.05199.5
1.69-1.787.10.72415030.7190.9150.30.7870.95799.6
1.78-1.896.90.56314840.8090.9460.2360.6130.93799.1
1.89-2.046.20.38114980.8780.9670.1690.4190.97398.2
2.04-2.247.90.27715170.9140.9770.1110.30.96799.5
2.24-2.5680.20415300.9610.990.080.221.03299.1
2.56-3.237.50.1515320.980.9950.0610.163198.3
3.23-507.50.10616520.9870.9970.0410.1140.97898.9

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.502→30.015 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2234 1490 10.03 %
Rwork0.1655 --
obs0.1713 14849 96.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.502→30.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms960 0 0 102 1062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005983
X-RAY DIFFRACTIONf_angle_d0.7991343
X-RAY DIFFRACTIONf_dihedral_angle_d12.43594
X-RAY DIFFRACTIONf_chiral_restr0.053149
X-RAY DIFFRACTIONf_plane_restr0.006178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5023-1.55080.2881180.1771058X-RAY DIFFRACTION85
1.5508-1.60620.27391300.15931136X-RAY DIFFRACTION94
1.6062-1.67050.22941300.16921185X-RAY DIFFRACTION95
1.6705-1.74660.24561330.17331202X-RAY DIFFRACTION97
1.7466-1.83860.26141360.15731214X-RAY DIFFRACTION97
1.8386-1.95380.22151380.15261228X-RAY DIFFRACTION98
1.9538-2.10460.20771360.14641221X-RAY DIFFRACTION98
2.1046-2.31640.21221380.15451237X-RAY DIFFRACTION99
2.3164-2.65140.25411390.17081260X-RAY DIFFRACTION99
2.6514-3.33980.23821410.17081269X-RAY DIFFRACTION98
3.3398-30.0150.20011510.17011349X-RAY DIFFRACTION99

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