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- PDB-5mj2: Extracellular domain of human CD83 - rhombohedral crystal form af... -

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Basic information

Entry
Database: PDB / ID: 5mj2
TitleExtracellular domain of human CD83 - rhombohedral crystal form after UV-RIP (S-SAD data)
ComponentsCD83 antigen
KeywordsIMMUNE SYSTEM / Dendritic cell / receptor / immunoglobulin
Function / homology
Function and homology information


positive regulation of CD4-positive, alpha-beta T cell differentiation / negative regulation of interleukin-4 production / CD4-positive, alpha-beta T cell differentiation / humoral immune response / positive regulation of interleukin-10 production / positive regulation of interleukin-2 production / defense response / external side of plasma membrane / signal transduction / plasma membrane
Similarity search - Function
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
DI(HYDROXYETHYL)ETHER / CD83 antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.98 Å
AuthorsKlingl, S. / Egerer-Sieber, C. / Schmid, B. / Weiler, S. / Muller, Y.A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB796 Germany
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Crystal Structure of the Extracellular Domain of the Human Dendritic Cell Surface Marker CD83.
Authors: Heilingloh, C.S. / Klingl, S. / Egerer-Sieber, C. / Schmid, B. / Weiler, S. / Muhl-Zurbes, P. / Hofmann, J. / Stump, J.D. / Sticht, H. / Kummer, M. / Steinkasserer, A. / Muller, Y.A.
History
DepositionNov 29, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant
Revision 2.0Nov 20, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CD83 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8732
Polymers12,7671
Non-polymers1061
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint3 kcal/mol
Surface area5380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.978, 62.978, 135.628
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-302-

HOH

21A-318-

HOH

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Components

#1: Protein CD83 antigen / hCD83 / B-cell activation protein / Cell surface protein HB15


Mass: 12766.979 Da / Num. of mol.: 1 / Mutation: C27S, C100S, C129S
Source method: isolated from a genetically manipulated source
Details: The first four residues (GSPG) are non-native residues of the linker which remains after the GST-tag was cleaved off. The third residue (P) was modeled as alanine due to missing electron ...Details: The first four residues (GSPG) are non-native residues of the linker which remains after the GST-tag was cleaved off. The third residue (P) was modeled as alanine due to missing electron density. The first and last two residues as well as the central region were not visible in the electron density maps.
Source: (gene. exp.) Homo sapiens (human) / Cell: Dendritic cells / Gene: CD83 / Plasmid: pGEX-2T / Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' / References: UniProt: Q01151
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.03 Å3/Da / Density % sol: 39.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 microliter protein (39 mg/ml in ultrapure water) and 0.4 microliter reservoir solution (0.2 M DL-malic acid (pH 7.0), 20% w/v PEG 3350) were mixed and equilibrated against 70 microliter ...Details: 0.2 microliter protein (39 mg/ml in ultrapure water) and 0.4 microliter reservoir solution (0.2 M DL-malic acid (pH 7.0), 20% w/v PEG 3350) were mixed and equilibrated against 70 microliter of reservoir solution Crystals appeared after ~13 months

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.800042 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.800042 Å / Relative weight: 1
ReflectionResolution: 1.98→45.21 Å / Num. obs: 14030 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 42.7 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 22.6
Reflection shellResolution: 1.98→2.1 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.677 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MxCuBEdata collection
XDSdata reduction
Cootmodel building
RefinementResolution: 1.98→45.21 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 21.06
RfactorNum. reflection% reflection
Rfree0.2059 702 5 %
Rwork0.1563 --
obs0.1587 14030 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.98→45.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms616 0 7 42 665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007673
X-RAY DIFFRACTIONf_angle_d1.067926
X-RAY DIFFRACTIONf_dihedral_angle_d11.569259
X-RAY DIFFRACTIONf_chiral_restr0.043110
X-RAY DIFFRACTIONf_plane_restr0.005119
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9782-2.13090.24481440.2282660X-RAY DIFFRACTION100
2.1309-2.34530.23591400.19352654X-RAY DIFFRACTION100
2.3453-2.68470.24711330.18282664X-RAY DIFFRACTION100
2.6847-3.38220.20571430.17222674X-RAY DIFFRACTION100
3.3822-45.22110.1841420.12742676X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0457-4.12282.90955.6038-4.06464.0550.47031.6869-0.284-0.8884-0.6354-0.68920.07071.40050.05950.3909-0.0402-0.0070.5595-0.03470.357334.384945.700247.4216
24.4327-0.7632-1.57947.03340.93974.0541-0.0082-0.1997-0.50760.54530.1084-0.38310.16240.0439-0.10180.3849-0.0067-0.09740.32-0.06230.383329.659439.517454.7491
32.4587-0.64060.833.48562.84593.8765-0.0546-0.0767-0.12840.21940.07010.11480.1040.2384-0.06790.2829-0.02270.0110.36130.0420.277521.229247.726357.1002
45.8173-2.8781-2.68483.23452.12925.8056-0.4113-0.2306-1.39740.92470.20.42421.09410.02770.16970.4365-0.0031-0.02940.3029-0.01710.517525.627736.397256.4688
53.3554-1.3467-1.48814.35672.17283.83130.00050.4024-0.5204-0.3323-0.04580.40450.1896-0.13210.020.3154-0.0329-0.04870.3726-0.03140.341722.326343.2549.4903
66.17940.5073-1.10074.8442-1.26346.20540.2326-0.33870.4803-0.13990.55120.5729-0.331-0.6619-0.70670.3188-0.02360.00270.4660.05320.49114.644355.454255.915
77.7521-1.80430.05994.058-2.12227.75990.03460.2956-0.822-0.7463-0.1924-1.27230.78080.69580.11370.42470.0020.03570.366-0.07010.460132.887938.271946.9189
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 18:24)
2X-RAY DIFFRACTION2(chain A and resid 25:38)
3X-RAY DIFFRACTION3(chain A and resid 39:88)
4X-RAY DIFFRACTION4(chain A and resid 89:98)
5X-RAY DIFFRACTION5(chain A and resid 99:110)
6X-RAY DIFFRACTION6(chain A and resid 111:120)
7X-RAY DIFFRACTION7(chain A and resid 121:129)

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