1XIW

Crystal structure of human CD3-e/d dimer in complex with a UCHT1 single-chain antibody fragment

> Summary

Summary for 1XIW

DescriptorT-cell surface glycoprotein CD3 epsilon chain, T-cell surface glycoprotein CD3 delta chain, immunoglobulin light chain variable region, immunoglobulin heavy chain variable region
Functional Keywordscd3-epsilon, cd3-delta, ucht1-scfv, immunoglobulin fold, antibody-antigen complex, membrane protein-immune system complex, membrane protein/immune system
Biological sourceHomo sapiens (human)
More
Cellular locationMembrane; Single-pass type I membrane protein P07766 P04234
Total number of polymer chains8
Total molecular weight93288.74
Authors
Arnett, K.L.,Harrison, S.C.,Wiley, D.C. (deposition date: 2004-09-22, release date: 2004-11-16, modification date: 2009-02-24)
Primary citation
Arnett, K.L.,Harrison, S.C.,Wiley, D.C.
Crystal structure of a human CD3-epsilon/delta dimer in complex with a UCHT1 single-chain antibody fragment.
Proc.Natl.Acad.Sci.USA, 101:16268-16273, 2004
PubMed: 15534202
DOI: 10.1073/pnas.0407359101
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (1.9 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.24070.5%1.0%4.7%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 1xiw
no rotation
Molmil generated image of 1xiw
rotated about x axis by 90°
Molmil generated image of 1xiw
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 1xiw
no rotation
Molmil generated image of 1xiw
rotated about x axis by 90°
Molmil generated image of 1xiw
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (1xiw.pdb1.gz [68.08 KB])
Coordinate files for Biological unit (1xiw.pdb2.gz [66.41 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, ET-cell surface glycoprotein CD3 epsilon chainpolymer10511893.12
UniProt (P07766)
Pfam (PF16681)
Homo sapiens (human)T-cell surface antigen T3/Leu-4 epsilon chain
B, FT-cell surface glycoprotein CD3 delta chainpolymer799106.52
UniProt (P04234)
Pfam (PF16680)
Homo sapiens (human)T-cell receptor T3 delta chain
C, Gimmunoglobulin light chain variable regionpolymer10811994.42
PIR (PH0888)
Mus musculus (house mouse)@PDBj
D, Himmunoglobulin heavy chain variable regionpolymer12213650.32
PIR (PH0887)
Mus musculus (house mouse)@PDBj
waterwater18.0319

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains8
Total molecular weight93288.7
Non-Polymers*Number of molecules0
Total molecular weight0.0
All*Total molecular weight93288.7
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.9 Å)
Cell axes64.87479.326150.747
Cell angles90.0090.0090.00
SpacegroupP 21 21 21
Resolution limits49.17 - 1.90
the highest resolution shell value2.020 - 1.900
R-factor0.204
R-work0.20400
the highest resolution shell value0.206
R-free0.24100
the highest resolution shell value0.273
RMSD bond length0.008
RMSD bond angle1.500

Data Collection Statistics

Resolution limits50.00 - 1.90
the highest resolution shell value -
Number of reflections60988
Rmerge_l_obs0.065
Completeness97.9
Redundancy4.9
the highest resolution shell value5.1
I/sigma(I)0

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP722

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
B0042105cellular_componentalpha-beta T cell receptor complex
B0005737cellular_componentcytoplasm
B0016021cellular_componentintegral component of membrane
B0005886cellular_componentplasma membrane
B0042101cellular_componentT cell receptor complex
B0046982molecular_functionprotein heterodimerization activity
B0003713molecular_functiontranscription coactivator activity
B0004888molecular_functiontransmembrane signaling receptor activity
B0007166biological_processcell surface receptor signaling pathway
B0045944biological_processpositive regulation of transcription from RNA polymerase II promoter
B0045059biological_processpositive thymic T cell selection
B0050776biological_processregulation of immune response
B0031295biological_processT cell costimulation
B0030217biological_processT cell differentiation
B0050852biological_processT cell receptor signaling pathway
F0042105cellular_componentalpha-beta T cell receptor complex
F0005737cellular_componentcytoplasm
F0016021cellular_componentintegral component of membrane
F0005886cellular_componentplasma membrane
F0042101cellular_componentT cell receptor complex
F0046982molecular_functionprotein heterodimerization activity
F0003713molecular_functiontranscription coactivator activity
F0004888molecular_functiontransmembrane signaling receptor activity
F0007166biological_processcell surface receptor signaling pathway
F0045944biological_processpositive regulation of transcription from RNA polymerase II promoter
F0045059biological_processpositive thymic T cell selection
F0050776biological_processregulation of immune response
F0031295biological_processT cell costimulation
F0030217biological_processT cell differentiation
F0050852biological_processT cell receptor signaling pathway
A0042105cellular_componentalpha-beta T cell receptor complex
A0005911cellular_componentcell-cell junction
A0009897cellular_componentexternal side of plasma membrane
A0001772cellular_componentimmunological synapse
A0005887cellular_componentintegral component of plasma membrane
A0005622cellular_componentintracellular
A0005886cellular_componentplasma membrane
A0042101cellular_componentT cell receptor complex
A0046982molecular_functionprotein heterodimerization activity
A0019901molecular_functionprotein kinase binding
A0030159molecular_functionreceptor signaling complex scaffold activity
A0005057molecular_functionreceptor signaling protein activity
A0017124molecular_functionSH3 domain binding
A0042608molecular_functionT cell receptor binding
A0004888molecular_functiontransmembrane signaling receptor activity
A0097190biological_processapoptotic signaling pathway
A0007166biological_processcell surface receptor signaling pathway
A0007186biological_processG-protein coupled receptor signaling pathway
A0010629biological_processnegative regulation of gene expression
A0045879biological_processnegative regulation of smoothened signaling pathway
A0045060biological_processnegative thymic T cell selection
A0046641biological_processpositive regulation of alpha-beta T cell proliferation
A0050850biological_processpositive regulation of calcium-mediated signaling
A0010628biological_processpositive regulation of gene expression
A0032729biological_processpositive regulation of interferon-gamma production
A0045086biological_processpositive regulation of interleukin-2 biosynthetic process
A0032753biological_processpositive regulation of interleukin-4 production
A0050731biological_processpositive regulation of peptidyl-tyrosine phosphorylation
A0002669biological_processpositive regulation of T cell anergy
A0042102biological_processpositive regulation of T cell proliferation
A0006461biological_processprotein complex assembly
A0042981biological_processregulation of apoptotic process
A0050776biological_processregulation of immune response
A0007584biological_processresponse to nutrient
A0007172biological_processsignal complex assembly
A0042110biological_processT cell activation
A0031295biological_processT cell costimulation
A0050852biological_processT cell receptor signaling pathway
A0007169biological_processtransmembrane receptor protein tyrosine kinase signaling pathway
E0042105cellular_componentalpha-beta T cell receptor complex
E0005911cellular_componentcell-cell junction
E0009897cellular_componentexternal side of plasma membrane
E0001772cellular_componentimmunological synapse
E0005887cellular_componentintegral component of plasma membrane
E0005622cellular_componentintracellular
E0005886cellular_componentplasma membrane
E0042101cellular_componentT cell receptor complex
E0046982molecular_functionprotein heterodimerization activity
E0019901molecular_functionprotein kinase binding
E0030159molecular_functionreceptor signaling complex scaffold activity
E0005057molecular_functionreceptor signaling protein activity
E0017124molecular_functionSH3 domain binding
E0042608molecular_functionT cell receptor binding
E0004888molecular_functiontransmembrane signaling receptor activity
E0097190biological_processapoptotic signaling pathway
E0007166biological_processcell surface receptor signaling pathway
E0007186biological_processG-protein coupled receptor signaling pathway
E0010629biological_processnegative regulation of gene expression
E0045879biological_processnegative regulation of smoothened signaling pathway
E0045060biological_processnegative thymic T cell selection
E0046641biological_processpositive regulation of alpha-beta T cell proliferation
E0050850biological_processpositive regulation of calcium-mediated signaling
E0010628biological_processpositive regulation of gene expression
E0032729biological_processpositive regulation of interferon-gamma production
E0045086biological_processpositive regulation of interleukin-2 biosynthetic process
E0032753biological_processpositive regulation of interleukin-4 production
E0050731biological_processpositive regulation of peptidyl-tyrosine phosphorylation
E0002669biological_processpositive regulation of T cell anergy
E0042102biological_processpositive regulation of T cell proliferation
E0006461biological_processprotein complex assembly
E0042981biological_processregulation of apoptotic process
E0050776biological_processregulation of immune response
E0007584biological_processresponse to nutrient
E0007172biological_processsignal complex assembly
E0042110biological_processT cell activation
E0031295biological_processT cell costimulation
E0050852biological_processT cell receptor signaling pathway
E0007169biological_processtransmembrane receptor protein tyrosine kinase signaling pathway
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Functional Information from PDB Data

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

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Functional Information from PROSITE/UniProt

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Functional Information from SwissProt/UniProt

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Catalytic Information from CSA

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Catalytic Information from CATRES

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> Sequence Neighbor

> Downloads

Resources

File formatFile name (file size)
PDBallpdb1xiw.ent.gz (135.31 KB)
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all (no-compress)pdb1xiw.ent (557.35 KB)
header onlypdb1xiw.ent.gz (8.38 KB)
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PDBx/mmCIF1xiw.cif.gz (166.06 KB)
PDBMLall1xiw.xml.gz (260.58 KB)
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no-atom1xiw-noatom.xml.gz (40.29 KB)
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ext-atom1xiw-extatom.xml.gz (149.78 KB)
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PDBMLplusall1xiw-plus.xml.gz (263.52 KB)
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no-atom1xiw-plus-noatom.xml.gz (43.24 KB)
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add only1xiw-add.xml.gz (2.95 KB)
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RDF1xiw.rdf.gz (81.83 KB)
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Structure factorsr1xiwsf.ent.gz (506.88 KB)
Biological unit (PDB format)1xiw.pdb1.gz (68.08 KB) (A,B,C,D)
*author defined assembly, 4 molecule(s) (tetrameric)
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1xiw.pdb2.gz (66.41 KB) (E,F,G,H)
*author defined assembly, 4 molecule(s) (tetrameric)
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Validation reportsPDF1xiw​_validation.pdf.gz (305.59 KB)
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PDF-full1xiw​_full​_validation.pdf.gz (316.19 KB)
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XML1xiw​_validation.xml.gz (33.65 KB)
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PNG1xiw​_multipercentile​_validation.png.gz (150.24 KB)
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SVG1xiw​_multipercentile​_validation.svg.gz (946 B)
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Sequence (fasta)1xiw​_seq.txt
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