1WZ9 - JenaLib

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Asymmetric Unit (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   THE 2.1 A STRUCTURE OF A TUMOUR SUPPRESSING SERPIN

Authors :   R. H. Law, J. A. Irving, A. M. Buckle, K. Ruzyla, M. Buzza, T. A. Bashtannyk-Puhalovich, T. C. Beddoe, N. Kim, D. M. Worrall, S. P. Bottomley, P. I. Bird, J. Rossjohn, J. C. Whisstock

Date :   03 Mar 05 (Deposition) - 15 Mar 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Maspin, Serpin, Tumor Suppressor, Serpinb5, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. H. Law, J. A. Irving, A. M. Buckle, K. Ruzyla, M. Buzza, T. A. Bashtannyk-Puhalovich, T. C. Beddoe, K. Nguyen, D. M. Worrall, S. P. Bottomley, P. I. Bird, J. Rossjohn, J. C. Whisstock
The High Resolution Crystal Structure Of The Human Tumor Suppressor Maspin Reveals A Novel Conformational Switch In The G-Helix.
J. Biol. Chem. V. 280 22356 2005
PubMed-ID: 15760906 | Reference-DOI: 10.1074/JBC.M412043200
(for further references see the PDB file header)

Molecule 1 - MASPIN PRECURSOR
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PRSETC
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	SERPINB5
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PROTEASE INHIBITOR 5

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 13)

No.	Name	Count	Type	Full Name
1	CME	12	Mod. Amino Acid	S,S-(2-HYDROXYETHYL)THIOCYSTEINE
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 7)

No.	Name	Count	Type	Full Name
1	CME	6	Mod. Amino Acid	S,S-(2-HYDROXYETHYL)THIOCYSTEINE
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 6)

No.	Name	Count	Type	Full Name
1	CME	6	Mod. Amino Acid	S,S-(2-HYDROXYETHYL)THIOCYSTEINE
2	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:26 , ASN A:27 , LYS A:280 , HOH A:1024 , GLY B:331 , ASP B:332	BINDING SITE FOR RESIDUE SO4 A 1001

(no "SS Bond" information available for 1WZ9)

(no "Cis Peptide Bond" information available for 1WZ9)

Asymmetric Unit (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_055223	S	176	P	SPB5_HUMAN	Polymorphism	2289519	A/B	P	176	P
2	UniProt	VAR_055224	V	187	L	SPB5_HUMAN	Polymorphism	2289520	A/B	L	187	L
3	UniProt	VAR_022115	I	319	V	SPB5_HUMAN	Polymorphism	1455555	A/B	I	319	V

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_055223	S	176	P	SPB5_HUMAN	Polymorphism	2289519	A	P	176	P
2	UniProt	VAR_055224	V	187	L	SPB5_HUMAN	Polymorphism	2289520	A	L	187	L
3	UniProt	VAR_022115	I	319	V	SPB5_HUMAN	Polymorphism	1455555	A	I	319	V

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_055223	S	176	P	SPB5_HUMAN	Polymorphism	2289519	B	P	176	P
2	UniProt	VAR_055224	V	187	L	SPB5_HUMAN	Polymorphism	2289520	B	L	187	L
3	UniProt	VAR_022115	I	319	V	SPB5_HUMAN	Polymorphism	1455555	B	I	319	V

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SERPIN	PS00284	Serpins signature.	SPB5_HUMAN	348-358	2	A:348-358 B:348-358

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SERPIN	PS00284	Serpins signature.	SPB5_HUMAN	348-358	1	A:348-358 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SERPIN	PS00284	Serpins signature.	SPB5_HUMAN	348-358	1	- B:348-358

Asymmetric Unit (6, 12)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000382771	1a	ENSE00001810765	chr18:61143994-61144278	285	SPB5_HUMAN	-	0	0	-	-
1.3	ENST00000382771	3	ENSE00002176461	chr18:61151655-61151829	175	SPB5_HUMAN	1-56	56	2	A:1-56 B:1-56	56 56
1.4	ENST00000382771	4	ENSE00001493317	chr18:61154179-61154316	138	SPB5_HUMAN	57-102	46	2	A:57-102 B:57-102	46 46
1.5b	ENST00000382771	5b	ENSE00001505282	chr18:61156580-61156697	118	SPB5_HUMAN	103-142	40	2	A:103-142 B:103-142	40 40
1.7a	ENST00000382771	7a	ENSE00001493314	chr18:61160186-61160328	143	SPB5_HUMAN	142-189	48	2	A:142-189 B:142-189 (gaps)	48 48
1.8	ENST00000382771	8	ENSE00001493312	chr18:61166353-61166520	168	SPB5_HUMAN	190-245	56	2	A:190-245 B:190-245 (gaps)	56 56
1.9c	ENST00000382771	9c	ENSE00001493310	chr18:61170563-61172318	1756	SPB5_HUMAN	246-375	130	2	A:246-375 (gaps) B:246-375 (gaps)	130 130

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:363
 aligned with SPB5_HUMAN | P36952 from UniProtKB/Swiss-Prot  Length:375

    Alignment length:375
                                    10        20        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     
           SPB5_HUMAN     1 MDALQLANSAFAVDLFKQLCEKEPLGNVLFSPICLSTSLSLAQVGAKGDTANEIGQVLHFENVKDVPFGFQTVTSDVNKLSSFYSLKLIKRLYVDKSLNLSTEFISSTKRPYAKELETVDFKDKLEETKGQINNSIKDLTDGHFENILADNSVNDQTKILVVNAAYFVGKWMKKFSESETKECPFRVNKTDTKPVQMMNMEATFCMGNIDSINCKIIELPFQNKHLSMFILLPKDVEDESTGLEKIEKQLNSESLSQWTNPSTMANAKVKLSIPKFKVEKMIDPKACLENLGLKHIFSEDTSDFSGMSETKGVALSNVIHKVCLEITEDGGDSIEVPGARILQHKDELNADHPFIYIIRHNKTRNIIFFGKFCSP 375
               SCOP domains d1wz9a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1wz9A01 A:1-169,A:276-327 Antithrombin, subunit I, domain 2                                                                                                              1wz9A02 A:170-275,A:328-375 Alpha-1-antitrypsin, domain 1                                                 1wz9A01 A:1-169,A:276-327                           1wz            9A02 A:170-275,A:328-375          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh...eeeeeeeeeee.hhh.hhhhhhhhh......eeee....hhhhhhhhhhhhhhhhh..................eeeeeeeeee.......hhhhheeeeee.....eeeeeeeeeeeeeeeeee....eeeeeee.hhh.eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeeeee.eeeeeeehhhhhhhhhh......................eeeeeeeeeeee....------------.eeeeee....eeeeeee....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P----------L-----------------------------------------------------------------------------------------------------------------------------------V-------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SERPIN     ----------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:1-56 UniProt: 1-56                     Exon 1.4  PDB: A:57-102 UniProt: 57-102       Exon 1.5b  PDB: A:103-142               -----------------------------------------------Exon 1.8  PDB: A:190-245 UniProt: 190-245               Exon 1.9c  PDB: A:246-375 (gaps) UniProt: 246-375                                                                                  Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------------------------Exon 1.7a  PDB: A:142-189 UniProt: 142-189      ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 1wz9 A   1 MDALQLANSAFAVDLFKQLcEKEPLGNVLFSPICLSTSLSLAQVGAKGDTANEIGQVLHFENVKDVPFGFQTVTSDVNKLSSFYSLKLIKRLYVDKSLNLSTEFISSTKRPYAKELETVDFKDKLEETKGQINNSIKDLTDGHFENILADNSVNDQTKILVVNAAYFVGKWMKKFPESETKEcPFRLNKTDTKPVQMMNMEATFcMGNIDSINcKIIELPFQNKHLSMFILLPKDVEDESTGLEKIEKQLNSESLSQWTNPSTMANAKVKLSIPKFKVEKMIDPKACLENLGLKHIFSEDTSDFSGMSETKGVALSNVIHKVcLEITEDG------------QHKDELNADHPFIYIIRHNKTRNIIFFGKFcSP 375
                                    10        20        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         -  |    350       360       370  |  
                                              20-CME                                                                                                                                                            183-CME               205-CME  214-CME                                                                                                      323-CME330          343                           373-CME

Chain B from PDB  Type:PROTEIN  Length:361
 aligned with SPB5_HUMAN | P36952 from UniProtKB/Swiss-Prot  Length:375

    Alignment length:375
                                    10        20        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     
           SPB5_HUMAN     1 MDALQLANSAFAVDLFKQLCEKEPLGNVLFSPICLSTSLSLAQVGAKGDTANEIGQVLHFENVKDVPFGFQTVTSDVNKLSSFYSLKLIKRLYVDKSLNLSTEFISSTKRPYAKELETVDFKDKLEETKGQINNSIKDLTDGHFENILADNSVNDQTKILVVNAAYFVGKWMKKFSESETKECPFRVNKTDTKPVQMMNMEATFCMGNIDSINCKIIELPFQNKHLSMFILLPKDVEDESTGLEKIEKQLNSESLSQWTNPSTMANAKVKLSIPKFKVEKMIDPKACLENLGLKHIFSEDTSDFSGMSETKGVALSNVIHKVCLEITEDGGDSIEVPGARILQHKDELNADHPFIYIIRHNKTRNIIFFGKFCSP 375
               SCOP domains d1wz9b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1wz9B01 B:1-169,B:276-327 Antithrombin, subunit I, domain 2                                                                                                              1wz9B02 B:170-275,B:328-375 Alpha-1-antitrypsin, domain 1                                                 1wz9B01 B:1-169,B:276-327                           1wz9B0        2 B:170-275,B:328-375              CATH domains
           Pfam domains (1) -----Serpin-1wz9B01 B:6-375                                                                                                                                                                                                                                                                                                                                                             Pfam domains (1)
           Pfam domains (2) -----Serpin-1wz9B02 B:6-375                                                                                                                                                                                                                                                                                                                                                             Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...eeeeeeeeeee.hhh.hhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhhh.........--.......eeeeeeeeee.......hhhhheeeeee.....eeeeeeeeeeeeeeeeee....eeeeeee.hhh.eeeeeeee...----.hhhhhhhh.hhhhhhhhhhhhhheeeeeeeeee.eeeeeee.hhhhhhhhh.hhhhh................eeeeeeeeeeee.......--------...eeeee....eeeeeee.....eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P----------L-----------------------------------------------------------------------------------------------------------------------------------V-------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SERPIN     ----------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: B:1-56 UniProt: 1-56                     Exon 1.4  PDB: B:57-102 UniProt: 57-102       Exon 1.5b  PDB: B:103-142               -----------------------------------------------Exon 1.8  PDB: B:190-245 (gaps) UniProt: 190-245        Exon 1.9c  PDB: B:246-375 (gaps) UniProt: 246-375                                                                                  Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------------------------Exon 1.7a  PDB: B:142-189 (gaps)                ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 1wz9 B   1 MDALQLANSAFAVDLFKQLcEKEPLGNVLFSPICLSTSLSLAQVGAKGDTANEIGQVLHFENVKDVPFGFQTVTSDVNKLSSFYSLKLIKRLYVDKSLNLSTEFISSTKRPYAKELETVDFKDKLEETKGQINNSIKDLTDGHFENILA--SVNDQTKILVVNAAYFVGKWMKKFPESETKEcPFRLNKTDTKPVQMMNMEATFcMGNIDSINcKIIELPFQNKHLSMFILLPKDV----TGLEKIEKQLNSESLSQWTNPSTMANAKVKLSIPKFKVEKMIDPKACLENLGLKHIFSEDTSDFSGMSETKGVALSNVIHKVcLEITEDGGDS--------LQHKDELNADHPFIYIIRHNKTRNIIFFGKFcSP 375
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140        |- |     160       170       180  |    190       200    |  210   |   220       230     |   -|      250       260       270       280       290       300       310       320  |    330  |      - |     350       360       370  |  
                                              20-CME                                                                                                                          149  |                            183-CME               205-CME  214-CME               236  241                                                                               323-CME   333      342                            373-CME
                                                                                                                                                                                 152

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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Multi-domain proteins (alpha and beta) (2421)

Fold: Serpins (120)

Superfamily: Serpins (120)

Family: Serpins (100)

Protein domain: automated matches (16)

Human (Homo sapiens) [TaxId: 9606] (15)

1a	d1wz9a_	A:
1b	d1wz9b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Antithrombin; Chain I, domain 2 (100)

Homologous Superfamily: Antithrombin, subunit I, domain 2 (100)

Human (Homo sapiens) (80)

1a	1wz9A01	A:1-169,A:276-327
1b	1wz9B01	B:1-169,B:276-327

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: Alpha-1-antitrypsin; domain 1 (101)

Homologous Superfamily: Alpha-1-antitrypsin, domain 1 (101)

Human (Homo sapiens) (81)

2a	1wz9A02	A:170-275,A:328-375
2b	1wz9B02	B:170-275,B:328-375

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Serpin] (63)

Family: Serpin (63)

Homo sapiens (Human) (41)

1a	Serpin-1wz9B01	B:6-375
1b	Serpin-1wz9B02	B:6-375

Asymmetric Unit(hide GO term definitions)

Chain A,B (SPB5_HUMAN | P36952)

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).
	GO:0004867	serine-type endopeptidase inhibitor activity	Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
	GO:0030198	extracellular matrix organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
	GO:0002009	morphogenesis of an epithelium	The process in which the anatomical structures of epithelia are generated and organized. An epithelium consists of closely packed cells arranged in one or more layers, that covers the outer surfaces of the body or lines any internal cavity or tube.
	GO:0006928	movement of cell or subcellular component	The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore.
	GO:0010951	negative regulation of endopeptidase activity	Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
	GO:0060512	prostate gland morphogenesis	The process in which the anatomical structures of a prostate gland are generated and organized.
	GO:0050678	regulation of epithelial cell proliferation	Any process that modulates the frequency, rate or extent of epithelial cell proliferation.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	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:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

Asymmetric Unit
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	1wz9
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	SPB5_HUMAN \| P36952	:	1xqg 1xqj 1xu8

1xu8	THE 2.8 A STRUCTURE OF A TUMOUR SUPRESSING SERPIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 13)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 6)

PROSITE Motifs (1, 2)

Exons (6, 12)

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SCOP Domains (1, 2)

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