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- PDB-7kp1: CD1a-42:2 SM binary complex -

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Basic information

Entry
Database: PDB / ID: 7kp1
TitleCD1a-42:2 SM binary complex
Components
  • Beta-2-microglobulin
  • T-cell surface glycoprotein CD1a
KeywordsIMMUNE SYSTEM / CD1 / antigen presentation / lipid
Function / homology
Function and homology information


endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression ...endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / specific granule lumen / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / endosome membrane / immune response / membrane raft / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
MHC-I family domain / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type ...MHC-I family domain / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
sphingomyelin / T-cell surface glycoprotein CD1a / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsWegrecki, M. / Le Nours, J. / Rossjohn, J.
CitationJournal: J.Exp.Med. / Year: 2021
Title: CD1a selectively captures endogenous cellular lipids that broadly block T cell response.
Authors: Cotton, R.N. / Wegrecki, M. / Cheng, T.Y. / Chen, Y.L. / Veerapen, N. / Le Nours, J. / Orgill, D.P. / Pomahac, B. / Talbot, S.G. / Willis, R. / Altman, J.D. / de Jong, A. / Van Rhijn, I. / ...Authors: Cotton, R.N. / Wegrecki, M. / Cheng, T.Y. / Chen, Y.L. / Veerapen, N. / Le Nours, J. / Orgill, D.P. / Pomahac, B. / Talbot, S.G. / Willis, R. / Altman, J.D. / de Jong, A. / Van Rhijn, I. / Clark, R.A. / Besra, G.S. / Ogg, G. / Rossjohn, J. / Moody, D.B.
History
DepositionNov 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: T-cell surface glycoprotein CD1a
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9044
Polymers44,8942
Non-polymers1,0092
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, CD1a:beta-2-microglobulin heterodimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-2 kcal/mol
Surface area19230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.148, 90.139, 105.961
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein T-cell surface glycoprotein CD1a / T-cell surface antigen T6/Leu-6 / hTa1 thymocyte antigen


Mass: 32464.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD1A / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P06126
#2: Protein Beta-2-microglobulin


Mass: 12429.966 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Homo sapiens (human) / References: UniProt: P61769
#3: Chemical ChemComp-FO4 / sphingomyelin


Mass: 814.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H94N2O6P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 45.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20-25% PEG 1500, 0.1M MMT pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.02→45.07 Å / Num. obs: 27297 / % possible obs: 100 % / Redundancy: 13.5 % / Biso Wilson estimate: 28.98 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.5
Reflection shellResolution: 2.02→2.07 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 1965 / CC1/2: 0.755 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NUX

6nux


Resolution: 2.02→45.07 Å / SU ML: 0.2332 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.3501
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2261 1301 4.78 %
Rwork0.1867 25937 -
obs0.1886 27238 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.35 Å2
Refinement stepCycle: LAST / Resolution: 2.02→45.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3045 0 68 224 3337
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00493207
X-RAY DIFFRACTIONf_angle_d0.82894355
X-RAY DIFFRACTIONf_chiral_restr0.0512446
X-RAY DIFFRACTIONf_plane_restr0.0041556
X-RAY DIFFRACTIONf_dihedral_angle_d21.35961151
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.10.29221580.2592798X-RAY DIFFRACTION99.97
2.1-2.20.24691360.22982841X-RAY DIFFRACTION100
2.2-2.310.25261250.21752852X-RAY DIFFRACTION100
2.31-2.460.25381450.21452843X-RAY DIFFRACTION100
2.46-2.650.2481560.20542856X-RAY DIFFRACTION100
2.65-2.910.25091570.20792838X-RAY DIFFRACTION100
2.91-3.330.25581370.18682902X-RAY DIFFRACTION100
3.33-4.20.18541460.16012927X-RAY DIFFRACTION100
4.2-45.070.19991410.16353080X-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)
15.61969683339-0.573631169534-0.6752733209731.90834315603-0.2081572904464.078260430750.03494257592660.682648368632-0.676907124676-0.304464855728-0.04286560561570.1584963778330.179818000622-0.287915123263-0.03144431621990.363956347271-0.05102760580650.02385774318250.287563734429-0.1204398918550.34425800450727.923721175830.937925978734.4676514212
22.737579148830.1944752881050.9135041501463.199018537381.108429041633.299936469660.05525260255590.01360797938960.2650977052320.02341326139440.1114250811960.01632628675060.0161928193426-0.0909934766017-0.1687392494670.1318786404980.01127497805830.009344920950860.160978701850.03430393426730.2317611930389.6779909450662.482844855850.743786494
32.81118986855-3.668297256370.2968071188574.934905651210.1169160244072.44270485753-0.202443197179-0.772207789170.248954371878-0.1047515243770.411388342216-0.512977421598-0.06486510268740.574280983208-0.1782153090560.2365460687260.0164255920233-0.02406711282350.38084294623-0.06689548239120.28750209112721.348194310843.876540372355.7130227531
41.728073237073.21731938771-2.811528073476.87932457359-3.503448555878.25799835773-0.3299485796350.1333283594310.4005947823860.2969487861870.5383966797240.695256662534-0.0561681647549-0.679949738695-0.1577688164630.2105353014530.0250030941817-0.0485273187350.3121517774850.049341343550.42964016723-2.2729270573250.876457625154.0529819257
53.02481427738-1.19868043844-2.593516793140.8183085667180.9898850133192.17199365614-0.153154907867-0.298669027863-0.3562478085420.0110385382750.08878255314210.1664358758770.1996793889570.1065024397210.1097531695760.1897127615360.00290443249665-0.02924612746620.1795394196840.03499948678930.25201305647114.205945218139.36264094155.1833445961
62.387045394891.719447873352.558408887024.03128652813.995036093654.39218908576-0.360884147768-1.22560738372-1.223480760540.884011416972-0.04855521829240.01588900537581.33980979014-0.6892399036820.4232925817140.4557253645510.02334731446210.06685008418240.4620170224740.07399515140220.3860585552284.6612539535935.994268626364.3828765938
75.180716001514.17114651083-4.608834786543.601462519-4.135547495235.06393275565-0.290251783268-0.0697710288392-0.946957025808-0.4654432393910.6943879673810.2888559378020.83147057553-0.742726291938-0.2825876090240.449102576347-0.0421765007686-0.1021928067650.2932037333170.09363549675190.5206887674367.0547291283933.369609893352.9306044194
83.5496052164-0.988782781063-3.044775641541.45402727620.4972245264212.32449560416-0.1739129908720.1696433761-0.356138535872-0.1464796216870.04612679633950.1789577427130.0832826924856-0.1002621677890.1240492289120.2243107018760.00702083299648-0.01172645269020.156793195435-0.01217791845510.2423729552416.489266481239.633672218448.4494889704
93.63602974331-2.51217736324-3.918914331887.503727762652.133915849644.28452185998-0.157960120486-1.391917156970.0697150622420.2648795023920.126451073492-0.0313570674866-0.851195859609-1.117363305570.1341002677810.4339185533710.04546357736760.04370712620450.51558283012-0.03119669154530.482992463927-1.2005909099946.269389176265.0921821443
103.96458432603-2.421749414181.44915105231.94635636077-1.025772127041.15519301953-0.42498238937-2.2003992937-0.111646135750.3982212091630.6357524573640.03173656938980.02023733545740.339274685639-0.1296568430250.299995292160.102951400297-0.02998344037590.5729404864850.03168087312850.2913485353217.606673938239.357511030963.5619039511
110.0956032030613-0.446604297925-0.3623663203435.346950759634.673799208394.13059213880.466087056364-1.077171493780.4189907044840.662904794662-0.1081331673250.120870392643-1.42182629339-0.653847585763-0.3907956949780.8031262091140.09324727928920.09468018652380.583102427526-0.1419856209830.4964178314711.4933733696355.97971058165.7385721242
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 181 )
2X-RAY DIFFRACTION2chain 'A' and (resid 182 through 285 )
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 12 )
4X-RAY DIFFRACTION4chain 'B' and (resid 13 through 20 )
5X-RAY DIFFRACTION5chain 'B' and (resid 21 through 42 )
6X-RAY DIFFRACTION6chain 'B' and (resid 43 through 47 )
7X-RAY DIFFRACTION7chain 'B' and (resid 48 through 52 )
8X-RAY DIFFRACTION8chain 'B' and (resid 53 through 72 )
9X-RAY DIFFRACTION9chain 'B' and (resid 73 through 78 )
10X-RAY DIFFRACTION10chain 'B' and (resid 79 through 95 )
11X-RAY DIFFRACTION11chain 'B' and (resid 96 through 105 )

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