1NPU - JenaLib

Title :   CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF MURINE PD-1

Authors :   X. Zhang, J. -C. D. Schwartz, X. Guo, E. Cao, L. Chen, Z. -Y. Zhang, S. G. Na S. C. Almo, S. K. Burley, New York Sgx Research Center For Struct Genomics (Nysgxrc)

Date :   20 Jan 03 (Deposition) - 23 Mar 04 (Release) - 26 Jan 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A

Keywords :   Ig V-Type Domain, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Zhang, J. C. Schwartz, X. Guo, S. Bhatia, E. Cao, M. Lorenz, M. Cammer L. Chen, Z. Y. Zhang, M. A. Edidin, S. G. Nathenson, S. C. Almo
Structural And Functional Analysis Of The Costimulatory Receptor Programmed Death-1.
Immunity V. 20 337 2004
PubMed-ID: 15030777 | Reference-DOI: 10.1016/S1074-7613(04)00051-2

Compounds

Molecule 1 - PROGRAMMED CELL DEATH PROTEIN 1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET3A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	IG V-TYPE DOMAIN
	Gene	:	PDCD1 OR PD1
	Mutation	:	YES
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	PROTEIN PD-1, MPD-1

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (1, 1)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological 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

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Chain A from PDB  Type:PROTEIN  Length:116
 aligned with PDCD1_MOUSE | Q02242 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:116
                                    43        53        63        73        83        93       103       113       123       133       143      
          PDCD1_MOUSE    34 SLTFYPAWLTVSEGANATFTCSLSNWSEDLMLNWNRLSPSNQTEKQAAFCNGLSQPVQDARFQIIQLPNRHDFHMNILDTRRNDSGIYLCGAISLHPKAKIEESPGAELVVTERIL 149
               SCOP domains d1npua_ A: Programmed cell death protein 1, PD1, extracellular domain                                                SCOP domains
               CATH domains 1npuA00 A:1-116 Immunoglobulins                                                                                      CATH domains
               Pfam domains V-set-1npuA01 A:1-112                                                                                           ---- Pfam domains
         Sec.struct. author .eeee..eeeee....eeeeeee.......eeeeeee.....eeeeeeee..eeee.....eeeee.....eeeeee...hhhhheeeeeeeee.....eeee...eeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 1npu A   1 SLTFYPAWLTVSEGANATFTCSLSNWSEDLMLNWNRLSPSNQTEKQAAFSNGLSQPVQDARFQIIQLPNRHDFHMNILDTRRNDSGIYLCGAISLHPKAKIEESPGAELVVTERIL 116
                                    10        20        30        40        50        60        70        80        90       100       110

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PDCD1_MOUSE | Q02242)

molecular function
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	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.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0002644	negative regulation of tolerance induction	Any process that stops, prevents, or reduces the frequency, rate, or extent of tolerance induction.
	GO:0070234	positive regulation of T cell apoptotic process	Any process that activates or increases the frequency, rate or extent of T cell death by apoptotic process.
	GO:0043065	positive regulation of apoptotic process	Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
cellular component
	GO:0009897	external side of plasma membrane	The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	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.

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	Cis Peptide Bonds
		Tyr A:5 - Pro A:6	[ RasMol ]

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