3NSJ - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   THE X-RAY CRYSTAL STRUCTURE OF LYMPHOCYTE PERFORIN

Authors :   R. H. Law, J. C. Whisstock, T. T. Caradoc-Davies

Date :   01 Jul 10 (Deposition) - 03 Nov 10 (Release) - 15 Dec 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.75

Chains :   Asym./Biol. Unit : A

Keywords :   Pore Forming Protein, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. H. Law, N. Lukoyanova, I. Voskoboinik, T. T. Caradoc-Davies, K. Baran, M. A. Dunstone, M. E. D'Angelo, E. V. Orlova, F. Coulibaly, S. Verschoor, K. A. Browne, A. Ciccone, M. J. Kuiper, P. I. Bird, J. A. Trapani, H. R. Saibil, J. C. Whisstock
The Structural Basis For Membrane Binding And Pore Formatio By Lymphocyte Perforin.
Nature V. 468 447 2010
PubMed-ID: 21037563 | Reference-DOI: 10.1038/NATURE09518

Molecule 1 - PERFORIN-1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Plasmid	:	PBACPAK9
	Expression System Strain	:	SF21
	Expression System Taxid	:	7108
	Expression System Vector Type	:	BACULOVIRUS
	Gene	:	PRF1, PFP
	Mutation	:	YES
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	P1, LYMPHOCYTE PORE-FORMING PROTEIN, CYTOLYSIN

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 12)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	CL	2	Ligand/Ion	CHLORIDE ION
3	GOL	3	Ligand/Ion	GLYCEROL
4	IOD	4	Ligand/Ion	IODIDE ION
5	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:448 , THR A:449 , VAL A:451 , ASP A:490	BINDING SITE FOR RESIDUE GOL A 652
02	AC2	SOFTWARE	GLY A:450 , VAL A:452 , TRP A:460 , THR A:461 , ASP A:462	BINDING SITE FOR RESIDUE GOL A 653
03	AC3	SOFTWARE	TRP A:373 , LEU A:541 , HOH A:1067	BINDING SITE FOR RESIDUE GOL A 654
04	AC4	SOFTWARE	ASP A:485 , TYR A:486 , TRP A:488 , ASP A:490 , HOH A:1053 , HOH A:1059	BINDING SITE FOR RESIDUE CA A 701
05	AC5	SOFTWARE	ASP A:435 , ASP A:483 , ALA A:484 , HOH A:955	BINDING SITE FOR RESIDUE CA A 702
06	AC6	SOFTWARE	VAL A:401 , ARG A:409 , GLN A:410	BINDING SITE FOR RESIDUE IOD A 712
07	AC7	SOFTWARE	PRO A:306 , SER A:309 , TRP A:327	BINDING SITE FOR RESIDUE IOD A 713
08	AC8	SOFTWARE	ARG A:498 , THR A:508	BINDING SITE FOR RESIDUE CL A 720
09	AC9	SOFTWARE	VAL A:417 , SER A:419 , TYR A:520 , HIS A:521	BINDING SITE FOR RESIDUE CL A 721
10	BC1	SOFTWARE	ASN A:202 , ASN A:204 , SER A:206	BINDING SITE FOR RESIDUE NAG A 722

Asymmetric/Biological Unit

No.	Residues
1	A:22	-	A:75
2	A:30	-	A:72
3	A:101	-	A:175
4	A:241	-	A:407
5	A:376	-	A:392
6	A:380	-	A:394
7	A:396	-	A:406
8	A:496	-	A:509
9	A:524	-	A:533

Asymmetric/Biological Unit

No.	Residues
1	Gly A:474	-	Gly A:475

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

Asymmetric/Biological Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MACPF_2	PS51412	Membrane attack complex/perforin (MACPF) domain profile.	PERF_MOUSE	26-374	1	A:26-374
2	MACPF_1	PS00279	Membrane attack complex/perforin (MACPF) domain signature.	PERF_MOUSE	211-222	1	A:211-222
3	C2	PS50004	C2 domain profile.	PERF_MOUSE	416-497	1	A:416-497

(no "Exon" information available for 3NSJ)

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

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:530
 aligned with PERF_MOUSE | P10820 from UniProtKB/Swiss-Prot  Length:554

    Alignment length:531
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550 
           PERF_MOUSE    21 PCYTATRSECKQKHKFVPGVWMAGEGMDVTTLRRSGSFPVNTQRFLRPDRTCTLCKNSLMRDATQRLPVAITHWRPHSSHCQRNVAAAKVHSTEGVAREAAANINNDWRVGLDVNPRPEANMRASVAGSHSKVANFAAEKTYQDQYNFNSDTVECRMYSFRLVQKPPLHLDFKKALRALPRNFNSSTEHAYHRLISSYGTHFITAVDLGGRISVLTALRTCQLTLNGLTADEVGDCLNVEAQVSIGAQASVSSEYKACEEKKKQHKMATSFHQTYRERHVEVLGGPLDSTHDLLFGNQATPEQFSTWTASLPSNPGLVDYSLEPLHTLLEEQNPKREALRQAISHYIMSRARWQNCSRPCRSGQHKSSHDSCQCECQDSKVTNQDCCPRQRGLAHLVVSNFRAEHLWGDYTTATDAYLKVFFGGQEFRTGVVWNNNNPRWTDKMDFENVLLSTGGPLRVQVWDADYGWDDDLLGSCDRSPHSGFHEVTCELNHGRVKFSYHAKCLPHLTGGTCLEYAPQGLLGDPPGNRSG 551
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------------------------------------------------------------------------------------------------------MACPF-3nsjA02 A:146-366                                                                                                                                                                                                      -------------------------------------------------C2-3nsjA01 A:416-497                                                              ------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeehhhhhhh......hhhhh..ee........................eeeee.......eeee...eeeeee.........eeeee.hhhhhhhhhhh.............-..............hhhhhhhhhhhhhh.eeeeeeeeeeeeeeeee......hhhhhhhhhh........hhhhhhhhhhhhh.eeeeeeeeeeeeeeeeeeehhhhhhh..hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh....hhhhhh..eeeeee..hhhhh.........hhhhhhhhhhhh....eeeeeeeee.hhhh....hhhhhhhhhhhhhhhhh.............eee.......eee......hhhhh.....eeeeeeeeeeee...........eeeeeee..eeee...............eeeeeee......eeeeeee.......eeeeeeee....eeeeeeee....eeeeeeeeee...ee.....ee............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----MACPF_2  PDB: A:26-374 UniProt: 26-374                                                                                                                                                                                                                                                                                                                       -----------------------------------------C2  PDB: A:416-497 UniProt: 416-497                                               ------------------------------------------------------ PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MACPF_1     ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nsj A  21 PCYTATRSECKQKHKFVPGVWMAGEGMDVTTLRRSGSFPVNTQRFLRPDRTCTLCKNSLMRDATQRLPVAITHWRPHSSHCQRNVAAAKVHSTEGVAREAAANINNDWRVGLDVN-RPEANMRASVAGSHSKVANFAAEKTYQDQYNFNSDTVECRMYSFRLVQKPPLHLDFKKALRALPRNFNSSTEHAYHELISSYGTHFITAVDLGGRISVLTALRTCQLTLNGLTADEVGDCLNVEAQVSIGAQASVSSEYKACEEKKKQHKMATSFHQTYRERHVEVLGGPLDSTHDLLFGNQATPEQFSTWTASLPSNPGLVDYSLEPLHTLLEEQNPKREALRQAISHYIMSRARWQNCSRPCRSGQHKSSHDSCQCECQDSKVTNQDCCPRQRGLAHLVVSNFRAEHLWGDYTTATDAYLKVFFGGQEFRTGVVWNNNNPRWTDKMDFENVLLSTGGPLRVQVWDADYGWDDDLLGSCDRSPHSGFHEVTCELNHGRVKFSYHAKCLPHLTGGTCLEYAPQGLLGDPPGNRSG 551
                                    30        40        50        60        70        80        90       100       110       120       130    | |140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550 
                                                                                                                                            135 |                                                                                                                                                                                                                                                                                                                                                                                                                              
                                                                                                                                              137

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 '\|'

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

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: C2 (71)

Family: C2 (34)

Mus musculus (Mouse) (4)

C2-3nsjA01

A:416-497

Clan: CDC (6)

Family: MACPF (3)

Mus musculus (Mouse) (1)

MACPF-3nsjA02

A:146-366

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PERF_MOUSE | P10820)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0022829	wide pore channel activity	Enables the transport of a solute across a membrane via a large pore, un-gated channel. Examples include gap junctions, which transport substances from one cell to another; and porins which transport substances in and out of bacteria, mitochondria and chloroplasts.
biological process
	GO:0019835	cytolysis	The rupture of cell membranes and the loss of cytoplasm.
	GO:0002357	defense response to tumor cell	Reactions triggered in response to the presence of a tumor cell that act to protect the cell or organism.
	GO:0051607	defense response to virus	Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
	GO:0002418	immune response to tumor cell	An immune system process that functions in the response of an organism to a tumor cell.
	GO:0001771	immunological synapse formation	The formation of an area of close contact between a lymphocyte (T-, B-, or natural killer cell) and a target cell through the clustering of particular signaling and adhesion molecules and their associated membrane rafts on both the lymphocyte and target cell, which facilitates activation of the lymphocyte, transfer of membrane from the target cell to the lymphocyte, and in some situations killing of the target cell through release of secretory granules and/or death-pathway ligand-receptor interaction.
	GO:0051260	protein homooligomerization	The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
	GO:0055085	transmembrane transport	The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
cellular component
	GO:0044194	cytolytic granule	A specialized secretory lysosome that is present in cells with cytolytic capability such as cytotoxic T lymphocytes and natural killer cells. Cytolytic granules mediate the storage and regulated excretion of lytic molecules for killing of target cells.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0031904	endosome lumen	The volume enclosed by the membrane of an endosome.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	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: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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly A:474 - Gly A:475	[ RasMol ]

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	3nsj
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	PERF_MOUSE \| P10820	:	4y1s 4y1t

(no "Related Entries Specified in the PDB File" available for 3NSJ)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 12)

Sites (10, 10)

SS Bonds (9, 9)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 3)

Exons (0, 0)

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