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(-) Description

Title :  42F3-P4B10/H2-LD
 
Authors :  J. J. Adams, D. M. Kranz, K. C. Garcia
Date :  15 Aug 11  (Deposition) - 07 Dec 11  (Release) - 18 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A,B,C,D  (2x)
Keywords :  Ig Mhc, Antigen Recognition, Tcr-Pmhc, Chimera Protein, Membrane Receptor, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. J. Adams, S. Narayanan, B. Liu, M. E. Birnbaum, A. C. Kruse, N. A. Bowerman, W. Chen, A. M. Levin, J. M. Connolly, C. Zhu, D. M. Kranz, K. C. Garcia
T Cell Receptor Signaling Is Limited By Docking Geometry To Peptide-Major Histocompatibility Complex.
Immunity V. 35 681 2011
PubMed-ID: 22101157  |  Reference-DOI: 10.1016/J.IMMUNI.2011.09.013

(-) Compounds

Molecule 1 - H2-LD SBM2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - P4B10 PEPTIDE
    Chains: B
    Engineered: YES
    Other Details: GENSCRIPT
    Synthetic: YES
 
Molecule 3 - 42F3 ALPHA
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: MUS MUSCULUS, HOMO SAPIENS
    Organism Taxid: 10090, 9606
    Other Details: MOUSE-HUMAN CHIMERA ALPHA CHAIN
 
Molecule 4 - 42F3 BETA
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: MUS MUSCULUS, HOMO SAPIENS
    Organism Taxid: 10090, 9606
    Other Details: MOUSE-HUMAN CHIMERA BETA CHAIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): ABCD
Biological Unit 2 (2x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NO31Ligand/IonNITRATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NO31Ligand/IonNITRATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1NO32Ligand/IonNITRATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:148 , GLN A:149 , TRP D:157 , ASN D:159 , GLY D:160 , HIS D:204 , ARG D:206BINDING SITE FOR RESIDUE NO3 D 242

(-) SS Bonds  (5, 5)

Asymmetric Unit
No.Residues
1A:101 -A:164
2C:22 -C:90
3C:161 -D:168
4D:23 -D:91
5D:142 -D:207

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser D:7 -Pro D:8
2Tyr D:148 -Pro D:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TFK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TFK)

(-) Exons   (0, 0)

(no "Exon" information available for 3TFK)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:174
 aligned with HA1L_MOUSE | P01897 from UniProtKB/Swiss-Prot  Length:362

    Alignment length:174
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195    
           HA1L_MOUSE    26 PHSMRYFETAVSRPGLGEPRYISVGYVDNKEFVRFDSDAENPRYEPQAPWMEQEGPEYWERITQIAKGQEQWFRVNLRTLLGYYNQSAGGTHTLQWMYGCDVGSDGRLLRGYEQFAYDGCDYIALNEDLKTWTAADMAAQITRRKWEQAGAAEYYRAYLEGECVEWLHRYLKNG 199
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeee........eeeeeeee..eeeeeee........ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeeeeee.....eeeeeeeeee..eeeeee......eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3tfk A   2 PHSMRYYETATSRRGLGEPRYTSVGYVDDKEFVRFDSDAENPRYEPQVPWMEQEGPEYWERITQVAKGQEQWFRVNLRTLLGYYNQSAGGTHTLQRMYGCDVGSDGRLLRGYEQFAYDGCDYIALNEDLRTWTAADMAAQITRRKWEQAGAAEYYRAYLEGECVEWLHRYLKNG 175
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171    


Chain B from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 3tfk B   1 QLSDVPMDL   9


Chain C from PDB  Type:PROTEIN  Length:201
                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeeee....eee..ee.....eeeeeeee......eeeeee.....eee....eeeeee....eeeeee...hhhhheeeeeeeee.......ee...eeeeee........eeeeeee......eeeeee................eee....eeehhhheee.eeeee...................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tfk C   0 AQSVTQPDARVTVSEGASLQLRCKYSYSATPYLFWYVQYPRQGLQMLLKYYSGDPVVQGVNGFEAEFSKSDSSFHLRKASVHWSDSAVYFCAVSAKGTGSKLSFGKGAKLTVSPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTF 200
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199 


Chain D from PDB  Type:PROTEIN  Length:239
                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeee....eeeeeee.....eeeeeeee...eeeeeeeee.....ee.......eee.....eeeeee...hhhhheeeeeeeeee..eeee...eeeeee.hhhhh...eeeeee.hhhhhhhhheeeeeeeeeee....eeeeeee..eee...eee....ee.........eeeeeeeeeehhhhh....eeeeeeee..................eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tfk D   3 AVTQSPRNKVTVTGGNVTLSCRQTNSHNYMYWYRQDTGHGLRLIHYSYGAGNLQIGDVPDGYKATRTTQEDFFLLLELASPSQTSLYFCASSDAPGQLYFGEGSKLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD 241
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3TFK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TFK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TFK)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A   (HA1L_MOUSE | P01897)
molecular function
    GO:0042605    peptide antigen binding    Interacting selectively and non-covalently with an antigen peptide.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
    GO:0019882    antigen processing and presentation    The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.
    GO:0002479    antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent    The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class I protein complex following intracellular transport via a TAP (transporter associated with antigen processing) pathway. The peptide is typically a fragment of a larger exogenous protein which has been degraded within the cell and is dependent on TAP transport from the cytosol to ER for association with the MHC class I molecule. Class I here refers to classical class I molecules.
    GO:0002474    antigen processing and presentation of peptide antigen via MHC class I    The process in which an antigen-presenting cell expresses a peptide antigen on its cell surface in association with an MHC class I protein complex. Class I here refers to classical class I molecules.
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
cellular component
    GO:0042612    MHC class I protein complex    A transmembrane protein complex composed of a MHC class I alpha chain and an invariant beta2-microglobin chain, and with or without a bound peptide antigen. Class I here refers to classical class I molecules.
    GO:0071556    integral component of lumenal side of endoplasmic reticulum membrane    The component of the endoplasmic reticulum membrane consisting of the gene products that penetrate only the lumenal side of the membrane.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0030670    phagocytic vesicle membrane    The lipid bilayer surrounding a phagocytic vesicle.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        HA1L_MOUSE | P01897: 1ld9 1ldp 2e7l 2oi9 3e2h 3e3q 3ery 3tf7 3tjh 3tpu 3uo1 3uyr 3v4u 3v52 3vj6 4ms8 4mvb 4mxq 4n0c 4n5e 4nhu

(-) Related Entries Specified in the PDB File

2oi9 2C QL9/H2-LD COMPLEX
3tf7
3tjh
3tpu