1CZV - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE C2 DOMAIN OF HUMAN COAGULATION FACTOR V: DIMERIC CRYSTAL FORM

Authors :   S. Macedo-Ribeiro, W. Bode, R. Huber, W. H. Kane, P. Fuentes-Prior

Date :   07 Sep 99 (Deposition) - 26 Nov 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Coagulation, Membrane-Binding, Discoidin Family, Calcium- Independent, Blood Clotting (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Macedo-Ribeiro, W. Bode, R. Huber, M. A. Quinn-Allen, S. W. Kim, T. L. Ortel, G. P. Bourenkov, H. D. Bartunik, M. T. Stubbs, W. H. Kane, P. Fuentes-Prior
Crystal Structures Of The Membrane-Binding C2 Domain Of Human Coagulation Factor V.
Nature V. 402 434 1999
PubMed-ID: 10586886 | Reference-DOI: 10.1038/46594
(for further references see the PDB file header)

Molecule 1 - PROTEIN (COAGULATION FACTOR V)
	Chains	:	A, B
	Engineered	:	YES
	Expression System Common	:	BACULOVIRUS-DRIVEN INSECT CELL SYSTEM
	Fragment	:	C2 DISCOIDIN-LIKE DOMAIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ACTIVATED PROTEIN C COFACTOR
	Tissue	:	BLOOD

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1CZV)

(no "Site" information available for 1CZV)

Asymmetric Unit

No.	Residues
1	A:1	-	A:156
2	B:1	-	B:156

Asymmetric Unit

No.	Residues
1	Asn A:128	-	Pro A:129
2	Asn B:128	-	Pro B:129

Asymmetric Unit (5, 10)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_032701	R	2102	C	FA5_HUMAN	Disease (FA5D)	118203910	A/B	R	37	C
2	UniProt	VAR_017329	R	2102	H	FA5_HUMAN	Disease (THPH2)	---	A/B	R	37	H
3	UniProt	VAR_021302	M	2148	T	FA5_HUMAN	Polymorphism	9332701	A/B	M	83	T
4	UniProt	VAR_034603	K	2185	R	FA5_HUMAN	Polymorphism	6679078	A/B	K	120	R
5	UniProt	VAR_013899	D	2222	G	FA5_HUMAN	Polymorphism	6027	A/B	D	157	G

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

Biological Unit 1 (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_032701	R	2102	C	FA5_HUMAN	Disease (FA5D)	118203910	A	R	37	C
2	UniProt	VAR_017329	R	2102	H	FA5_HUMAN	Disease (THPH2)	---	A	R	37	H
3	UniProt	VAR_021302	M	2148	T	FA5_HUMAN	Polymorphism	9332701	A	M	83	T
4	UniProt	VAR_034603	K	2185	R	FA5_HUMAN	Polymorphism	6679078	A	K	120	R
5	UniProt	VAR_013899	D	2222	G	FA5_HUMAN	Polymorphism	6027	A	D	157	G

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

Biological Unit 2 (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_032701	R	2102	C	FA5_HUMAN	Disease (FA5D)	118203910	B	R	37	C
2	UniProt	VAR_017329	R	2102	H	FA5_HUMAN	Disease (THPH2)	---	B	R	37	H
3	UniProt	VAR_021302	M	2148	T	FA5_HUMAN	Polymorphism	9332701	B	M	83	T
4	UniProt	VAR_034603	K	2185	R	FA5_HUMAN	Polymorphism	6679078	B	K	120	R
5	UniProt	VAR_013899	D	2222	G	FA5_HUMAN	Polymorphism	6027	B	D	157	G

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

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FA58C_3	PS50022	Coagulation factors 5/8 type C domain (FA58C) profile.	FA5_HUMAN	1907-2061 2066-2221	2	- A:1-156 B:1-156
2	FA58C_1	PS01285	Coagulation factors 5/8 type C domain (FA58C) signature 1.	FA5_HUMAN	1947-1980 2111-2140	2	- A:46-75 B:46-75
3	FA58C_2	PS01286	Coagulation factors 5/8 type C domain (FA58C) signature 2.	FA5_HUMAN	2045-2061 2205-2221	2	- A:140-156 B:140-156

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FA58C_3	PS50022	Coagulation factors 5/8 type C domain (FA58C) profile.	FA5_HUMAN	1907-2061 2066-2221	1	- A:1-156 -
2	FA58C_1	PS01285	Coagulation factors 5/8 type C domain (FA58C) signature 1.	FA5_HUMAN	1947-1980 2111-2140	1	- A:46-75 -
3	FA58C_2	PS01286	Coagulation factors 5/8 type C domain (FA58C) signature 2.	FA5_HUMAN	2045-2061 2205-2221	1	- A:140-156 -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FA58C_3	PS50022	Coagulation factors 5/8 type C domain (FA58C) profile.	FA5_HUMAN	1907-2061 2066-2221	1	- - B:1-156
2	FA58C_1	PS01285	Coagulation factors 5/8 type C domain (FA58C) signature 1.	FA5_HUMAN	1947-1980 2111-2140	1	- - B:46-75
3	FA58C_2	PS01286	Coagulation factors 5/8 type C domain (FA58C) signature 2.	FA5_HUMAN	2045-2061 2205-2221	1	- - B:140-156

Asymmetric Unit (3, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000367797	1	ENSE00001673787	chr1:169555826-169555467	360	FA5_HUMAN	1-53	53	0	-	-
1.2	ENST00000367797	2	ENSE00000789613	chr1:169551760-169551669	92	FA5_HUMAN	53-84	32	0	-	-
1.3	ENST00000367797	3	ENSE00000789612	chr1:169541581-169541459	123	FA5_HUMAN	84-125	42	0	-	-
1.4	ENST00000367797	4	ENSE00000789611	chr1:169530004-169529792	213	FA5_HUMAN	125-196	72	0	-	-
1.5	ENST00000367797	5	ENSE00000789610	chr1:169528534-169528391	144	FA5_HUMAN	196-244	49	0	-	-
1.6	ENST00000367797	6	ENSE00001435704	chr1:169526105-169525884	222	FA5_HUMAN	244-318	75	0	-	-
1.7	ENST00000367797	7	ENSE00001435673	chr1:169524585-169524420	166	FA5_HUMAN	318-373	56	0	-	-
1.8	ENST00000367797	8	ENSE00000789607	chr1:169521972-169521795	178	FA5_HUMAN	373-432	60	0	-	-
1.9	ENST00000367797	9	ENSE00000789606	chr1:169519977-169519878	100	FA5_HUMAN	433-466	34	0	-	-
1.10	ENST00000367797	10	ENSE00000789605	chr1:169519253-169519039	215	FA5_HUMAN	466-537	72	0	-	-
1.11	ENST00000367797	11	ENSE00000789604	chr1:169515830-169515680	151	FA5_HUMAN	538-588	51	0	-	-
1.12b	ENST00000367797	12b	ENSE00000789603	chr1:169513746-169513534	213	FA5_HUMAN	588-659	72	0	-	-
1.13	ENST00000367797	13	ENSE00000814494	chr1:169512352-169509532	2821	FA5_HUMAN	659-1599	941	0	-	-
1.14	ENST00000367797	14	ENSE00000814495	chr1:169505918-169505744	175	FA5_HUMAN	1599-1657	59	0	-	-
1.15	ENST00000367797	15	ENSE00000814496	chr1:169500260-169500024	237	FA5_HUMAN	1658-1736	79	0	-	-
1.16	ENST00000367797	16	ENSE00001376235	chr1:169499056-169498846	211	FA5_HUMAN	1737-1807	71	0	-	-
1.17	ENST00000367797	17	ENSE00001388919	chr1:169497332-169497153	180	FA5_HUMAN	1807-1867	61	0	-	-
1.18	ENST00000367797	18	ENSE00001367181	chr1:169495255-169495139	117	FA5_HUMAN	1867-1906	40	0	-	-
1.19	ENST00000367797	19	ENSE00001168291	chr1:169494146-169494075	72	FA5_HUMAN	1906-1930	25	0	-	-
1.20	ENST00000367797	20	ENSE00001168281	chr1:169493142-169493039	104	FA5_HUMAN	1930-1964	35	0	-	-
1.21	ENST00000367797	21	ENSE00000814502	chr1:169492590-169492435	156	FA5_HUMAN	1965-2016	52	0	-	-
1.22	ENST00000367797	22	ENSE00000814503	chr1:169489902-169489758	145	FA5_HUMAN	2017-2065	49	0	-	-
1.23	ENST00000367797	23	ENSE00001168273	chr1:169487801-169487650	152	FA5_HUMAN	2065-2115	51	2	A:1-50 B:1-50	50 50
1.24b	ENST00000367797	24b	ENSE00000814505	chr1:169484864-169484682	183	FA5_HUMAN	2116-2176	61	2	A:51-111 B:51-111	61 61
1.25	ENST00000367797	25	ENSE00001627321	chr1:169483697-169483404	294	FA5_HUMAN	2177-2224	48	2	A:112-159 B:112-159	48 48

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:159
 aligned with FA5_HUMAN | P12259 from UniProtKB/Swiss-Prot  Length:2224

    Alignment length:159
                                  2075      2085      2095      2105      2115      2125      2135      2145      2155      2165      2175      2185      2195      2205      2215         
           FA5_HUMAN   2066 CSTPLGMENGKIENKQITASSFKKSWWGDYWEPFRARLNAQGRVNAWQAKANNNKQWLEIDLLKIKKITAIITQGCKSLSSEMYVKSYTIHYSEQGVEWKPYRLKSSMVDKIFEGNTNTKGHVKNFFNPPIISRFIRVIPKTWNQSIALRLELFGCDIY 2224
               SCOP domains d1czva_ A: C2 domain of factor V                                                                                                                                SCOP domains
               CATH domains 1czvA00 A:1-159 Galactose-binding domain-like                                                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhheeeee...........hhhhh....................eeeee........eeeeee.........eeeeeeeee...................eeeee.....eeeee.......eeeee..........eeeee..... Sec.struct. author
             SAPs(SNPs) (1) ------------------------------------C---------------------------------------------T------------------------------------R------------------------------------G-- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------H-------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                PROSITE (1) FA58C_3  PDB: A:1-156 UniProt: 2066-2221                                                                                                                    --- PROSITE (1)
                PROSITE (2) ---------------------------------------------FA58C_1  PDB: A:46-75         ----------------------------------------------------------------FA58C_2          --- PROSITE (2)
               Transcript 1 Exon 1.23  PDB: A:1-50 UniProt: 2065-2115         Exon 1.24b  PDB: A:51-111 UniProt: 2116-2176                 Exon 1.25  PDB: A:112-159 UniProt: 2177-2224     Transcript 1
                1czv A    1 CSTPLGMENGKIENKQITASSFKKSWWGDYWEPFRARLNAQGRVNAWQAKANNNKQWLEIDLLKIKKITAIITQGCKSLSSEMYVKSYTIHYSEQGVEWKPYRLKSSMVDKIFEGNTNTKGHVKNFFNPPIISRFIRVIPKTWNQSITLRLELFGCDIY  159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain B from PDB  Type:PROTEIN  Length:159
 aligned with FA5_HUMAN | P12259 from UniProtKB/Swiss-Prot  Length:2224

    Alignment length:159
                                  2075      2085      2095      2105      2115      2125      2135      2145      2155      2165      2175      2185      2195      2205      2215         
           FA5_HUMAN   2066 CSTPLGMENGKIENKQITASSFKKSWWGDYWEPFRARLNAQGRVNAWQAKANNNKQWLEIDLLKIKKITAIITQGCKSLSSEMYVKSYTIHYSEQGVEWKPYRLKSSMVDKIFEGNTNTKGHVKNFFNPPIISRFIRVIPKTWNQSIALRLELFGCDIY 2224
               SCOP domains d1czvb_ B: C2 domain of factor V                                                                                                                                SCOP domains
               CATH domains 1czvB00 B:1-159 Galactose-binding domain-like                                                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhheeeee...........hhhhh....................eeeee........eeeeee.........eeeeeeeee...................eeeee.....eeeee.......eeeee..........eeeee..... Sec.struct. author
             SAPs(SNPs) (1) ------------------------------------C---------------------------------------------T------------------------------------R------------------------------------G-- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------H-------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                PROSITE (1) FA58C_3  PDB: B:1-156 UniProt: 2066-2221                                                                                                                    --- PROSITE (1)
                PROSITE (2) ---------------------------------------------FA58C_1  PDB: B:46-75         ----------------------------------------------------------------FA58C_2          --- PROSITE (2)
               Transcript 1 Exon 1.23  PDB: B:1-50 UniProt: 2065-2115         Exon 1.24b  PDB: B:51-111 UniProt: 2116-2176                 Exon 1.25  PDB: B:112-159 UniProt: 2177-2224     Transcript 1
                1czv B    1 CSTPLGMENGKIENKQITASSFKKSWWGDYWEPFRARLNAQGRVNAWQAKANNNKQWLEIDLLKIKKITAIITQGCKSLSSEMYVKSYTIHYSEQGVEWKPYRLKSSMVDKIFEGNTNTKGHVKNFFNPPIISRFIRVIPKTWNQSITLRLELFGCDIY  159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Legend:		→ Mismatch	(orange background)
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	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( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Galactose-binding domain-like (314)

Superfamily: Galactose-binding domain-like (314)

Family: Discoidin domain (FA58C, coagulation factor 5/8 C-terminal domain) (17)

Protein domain: C2 domain of factor V (4)

Human (Homo sapiens) [TaxId: 9606] (3)

1a	d1czva_	A:
1b	d1czvb_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

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Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: Galactose-binding domain-like (195)

Human (Homo sapiens) (39)

1a	1czvA00	A:1-159
1b	1czvB00	B:1-159

(no "Pfam Domain" information available for 1CZV)

Asymmetric Unit(hide GO term definitions)

Chain A,B (FA5_HUMAN | P12259)

molecular function
	GO:0005507	copper ion binding	Interacting selectively and non-covalently with copper (Cu) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0048208	COPII vesicle coating	The addition of COPII proteins and adaptor proteins to ER membranes during the formation of transport vesicles, forming a vesicle coat.
	GO:0006888	ER to Golgi vesicle-mediated transport	The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
	GO:0008015	blood circulation	The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products.
	GO:0007596	blood coagulation	The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
	GO:0007599	hemostasis	The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
	GO:0030168	platelet activation	A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.
	GO:0002576	platelet degranulation	The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
cellular component
	GO:0030134	COPII-coated ER to Golgi transport vesicle	A vesicle with a coat formed of the COPII coat complex proteins. The COPII coat complex is formed by the Sec23p/Sec24p and the Sec13p/Sec31p heterodimers. COPII-associated vesicles transport proteins from the rough endoplasmic reticulum to the Golgi apparatus (anterograde transport).
	GO:0000139	Golgi membrane	The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
	GO:0005788	endoplasmic reticulum lumen	The volume enclosed by the membranes of the endoplasmic reticulum.
	GO:0033116	endoplasmic reticulum-Golgi intermediate compartment membrane	The lipid bilayer surrounding any of the compartments of the endoplasmic reticulum (ER)-Golgi intermediate compartment system.
	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.
	GO:1903561	extracellular vesicle	Any vesicle that is part of the extracellular region.
	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.
	GO:0031091	platelet alpha granule	A secretory organelle found in blood platelets, which is unique in that it exhibits further compartmentalization and acquires its protein content via two distinct mechanisms: (1) biosynthesis predominantly at the megakaryocyte (MK) level (with some vestigial platelet synthesis) (e.g. platelet factor 4) and (2) endocytosis and pinocytosis at both the MK and circulating platelet levels (e.g. fibrinogen (Fg) and IgG).
	GO:0031093	platelet alpha granule lumen	The volume enclosed by the membrane of the platelet alpha granule.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1czv)

	Sites
(no "Sites" information available for 1czv)

	Cis Peptide Bonds
		Asn A:128 - Pro A:129	[ RasMol ]
		Asn B:128 - Pro B:129	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	1czv
		Family and Domain Information	:	ProDom \| SYSTERS
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	FA5_HUMAN \| P12259
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	188055
		Disease Information	:	OMIM
	227400
		Disease Information	:	OMIM

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	FA5_HUMAN \| P12259
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UniProtKB/Swiss-Prot
	FA5_HUMAN \| P12259	:	1czs 1czt 1fv4 1y61 3p6z 3p70 3s9c

1czs	PHENYLMERCURY COMPLEX-MONOMERIC CRYSTAL FORM
1czt	NATIVE MONOMERIC CRYSTAL FORM

Description

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Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (2, 2)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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Exons (3, 6)

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SCOP Domains (1, 2)

CATH Domains (1, 2)

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