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Title :   COMBINED HIGH- AND LOW-RESOLUTION TECHNIQUES REVEAL COMPACT STRUCTURE IN CENTRAL PORTION OF FACTOR H DESPITE LONG INTER-MODULAR LINKERS

Authors :   C. Q. Schmidt, A. P. Herbert, M. Guariento, H. D. T. Mertens, D. C. Soares, D. Uhrin, A. J. Rowe, D. I. Svergun, P. N. Barlow

Date :   04 Aug 09 (Deposition) - 03 Nov 09 (Release) - 08 Dec 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Compact Structure, Limited Interdomain Flexibility, Age- Related Macular Degeneration, Alternative Splicing, Complement Alternate Pathway, Disease Mutation, Disulfide Bond, Glycoprotein, Immune Response, Innate Immunity, Polymorphism, Secreted, Sushi, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Q. Schmidt, A. P. Herbert, H. D. T. Mertens, M. Guariento, D. C. Soares, D. Uhrin, A. J. Rowe, D. I. Svergun, P. N. Barlow
The Central Portion Of Factor H (Modules 10-15) Is Compact And Contains A Structurally Deviant Ccp Module
J. Mol. Biol. V. 395 105 2010
PubMed-ID: 19835885 | Reference-DOI: 10.1016/J.JMB.2009.10.010
(for further references see the PDB file header)

Molecule 1 - COMPLEMENT FACTOR H
	Chains	:	A
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Strain	:	KM71H
	Expression System Taxid	:	4922
	Expression System Vector	:	PPICZALPHAB
	Expression System Vector Type	:	VECTOR
	Fragment	:	SUSHI DOMAIN, RESIDUES 690-804
	Gene	:	CFH, HF, HF1, HF2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	H FACTOR 1


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2KMS)

(no "Site" information available for 2KMS)

NMR Structure

No.	Residues
1	A:691	-	A:733
2	A:719	-	A:744
3	A:753	-	A:792
4	A:781	-	A:803

NMR Structure

No.	Model	Residues
1	1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20	Pro A:707	-	Pro A:708
2	1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20	Asp A:798	-	Pro A:799

(no "SAP(SNP)/Variant" information available for 2KMS)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SUSHI	PS50923	Sushi/CCP/SCR domain profile.	CFAH_HUMAN	19-82 83-143 144-207 208-264 265-322 387-444 446-507 515-566 567-625 628-686 689-746 751-805 809-866 868-928 929-986 987-1045 1046-1104 1107-1165 1194-1230	1	- - - - - - - - - - - A:751-804 - - - - - - -

NMR Structure (2, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000367429	1a	ENSE00001444484	chr1:196621008-196621305	298	CFAH_HUMAN	1-20	20	0	-	-
1.2a	ENST00000367429	2a	ENSE00001134426	chr1:196642108-196642293	186	CFAH_HUMAN	20-82	63	0	-	-
1.3	ENST00000367429	3	ENSE00000791013	chr1:196642987-196643092	106	CFAH_HUMAN	82-117	36	0	-	-
1.4	ENST00000367429	4	ENSE00000791014	chr1:196645119-196645195	77	CFAH_HUMAN	117-143	27	0	-	-
1.5b	ENST00000367429	5b	ENSE00000469039	chr1:196646606-196646797	192	CFAH_HUMAN	143-207	65	0	-	-
1.5c	ENST00000367429	5c	ENSE00000791016	chr1:196648753-196648923	171	CFAH_HUMAN	207-264	58	0	-	-
1.6	ENST00000367429	6	ENSE00000469041	chr1:196654194-196654367	174	CFAH_HUMAN	264-322	59	0	-	-
1.7	ENST00000367429	7	ENSE00001769047	chr1:196658550-196658744	195	CFAH_HUMAN	322-387	66	0	-	-
1.8a	ENST00000367429	8a	ENSE00001597868	chr1:196659193-196659369	177	CFAH_HUMAN	387-446	60	0	-	-
1.12	ENST00000367429	12	ENSE00000469044	chr1:196682865-196683047	183	CFAH_HUMAN	446-507	62	0	-	-
1.13	ENST00000367429	13	ENSE00000469045	chr1:196684723-196684899	177	CFAH_HUMAN	507-566	60	0	-	-
1.14	ENST00000367429	14	ENSE00000791022	chr1:196694251-196694427	177	CFAH_HUMAN	566-625	60	0	-	-
1.15	ENST00000367429	15	ENSE00000791023	chr1:196695600-196695782	183	CFAH_HUMAN	625-686	62	0	-	-
1.16	ENST00000367429	16	ENSE00000469048	chr1:196695891-196696070	180	CFAH_HUMAN	686-746	61	1	A:690-746	57
1.17	ENST00000367429	17	ENSE00000791025	chr1:196697476-196697652	177	CFAH_HUMAN	746-805	60	1	A:746-804	59
1.18a	ENST00000367429	18a	ENSE00000791026	chr1:196705954-196706136	183	CFAH_HUMAN	805-866	62	0	-	-
1.19	ENST00000367429	19	ENSE00000791027	chr1:196706605-196706790	186	CFAH_HUMAN	866-928	63	0	-	-
1.20a	ENST00000367429	20a	ENSE00000791028	chr1:196709749-196709922	174	CFAH_HUMAN	928-986	59	0	-	-
1.20d	ENST00000367429	20d	ENSE00000469053	chr1:196711005-196711181	177	CFAH_HUMAN	986-1045	60	0	-	-
1.21	ENST00000367429	21	ENSE00001622338	chr1:196712582-196712758	177	CFAH_HUMAN	1045-1104	60	0	-	-
1.22	ENST00000367429	22	ENSE00001719380	chr1:196714947-196715129	183	CFAH_HUMAN	1104-1165	62	0	-	-
1.23	ENST00000367429	23	ENSE00001931000	chr1:196716241-196716634	394	CFAH_HUMAN	1165-1231	67	0	-	-

NMR Structure

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
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Chain A from PDB  Type:PROTEIN  Length:115
 aligned with CFAH_HUMAN | P08603 from UniProtKB/Swiss-Prot  Length:1231

    Alignment length:115
                                   699       709       719       729       739       749       759       769       779       789       799     
           CFAH_HUMAN   690 TCGDIPELEHGWAQLSSPPYYYGDSVEFNCSESFTMIGHRSITCIHGVWTQLPQCVAIDKLKKCKSSNLIILEEHLKNKKEFDHNSNIRYRCRGKEGWIHTVCINGRWDPEVNCS 804
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2kmsA01 A:690-746 Complement Module, domain 1            ---------------------------------------------------------- CATH domains
               Pfam domains -Sushi-2kmsA01 A:691-744                               ------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........ee...........eeeee...........eee....................ee.........hhhhh.ee....ee............eee....ee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE SUSHI  PDB: - UniProt: 689-746                           ----SUSHI  PDB: A:751-804 UniProt: 751-805                 PROSITE
           Transcript 1 (1) Exon 1.16  PDB: A:690-746 UniProt: 686-746 [INCOMPLETE]  ---------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------Exon 1.17  PDB: A:746-804 UniProt: 746-805 [INCOMPLETE]     Transcript 1 (2)
                 2kms A 690 TCGDIPELEHGWAQLSSPPYYYGDSVEFNCSESFTMIGHRSITCIHGVWTQLPQCVAIDKLKKCKSSNLIILEEHLKNKKEFDHNSNIRYRCRGKEGWIHTVCINGRWDPEVNCS 804
                                   699       709       719       729       739       749       759       769       779       789       799

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 2KMS)

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Ribbon (789)

Topology: Complement Module; domain 1 (62)

Homologous Superfamily: Complement Module, domain 1 (60)

Human (Homo sapiens) (46)

2kmsA01

A:690-746

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Sushi] (50)

Family: Sushi (50)

Homo sapiens (Human) (42)

Sushi-2kmsA01

A:691-744

NMR Structure(hide GO term definitions)

Chain A (CFAH_HUMAN | P08603)

molecular function
	GO:0043395	heparan sulfate proteoglycan binding	Interacting selectively and non-covalently with a heparan sulfate proteoglycan, any proteoglycan containing heparan sulfate as the glycosaminoglycan carbohydrate unit.
	GO:0008201	heparin binding	Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
	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:0006956	complement activation	Any process involved in the activation of any of the steps of the complement cascade, which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes; the initial steps of complement activation involve one of three pathways, the classical pathway, the alternative pathway, and the lectin pathway, all of which lead to the terminal complement pathway.
	GO:0006957	complement activation, alternative pathway	Any process involved in the activation of any of the steps of the alternative pathway of the complement cascade which allows for the direct killing of microbes and the regulation of other immune processes.
	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:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0030449	regulation of complement activation	Any process that modulates the frequency, rate or extent of complement activation.
cellular component
	GO:0072562	blood microparticle	A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
	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.

NMR Structure
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	Cis Peptide Bonds
		Asp A:798 - Pro A:799	[ RasMol ]
		Pro A:707 - Pro A:708	[ RasMol ]

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Description

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SS Bonds (4, 4)

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