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Description

Title :   CRYSTAL STRUCTURE OF HUMAN COMPLEMENT FACTOR H, SCR DOMAINS 6-8 (H402 RISK VARIANT), IN COMPLEX WITH LIGAND.

Authors :   B. E. Prosser, S. Johnson, P. Roversi, A. P. Herbert, B. S. Blaum, J. Tyrrell, T. A. Jowitt, S. J. Clark, E. Tarelli, D. Uhrin, P. N. Barlow, R. B. Sim, A. J. Day, S. M. Lea

Date :   07 Aug 07 (Deposition) - 02 Oct 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A

Keywords :   Alternative Splicing, Sucrose Octasulphate, Age-Related Macular Degeneration, Sushi, Secreted, Factor H, Complement, Polymorphism, Complement Alternate Pathway, Immune System, Disease Mutation, Glycosaminoglycan, Glycoprotein, Innate Immunity, Immune Response (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. E. Prosser, S. Johnson, P. Roversi, A. P. Herbert, B. S. Blaum, J. Tyrrell, T. A. Jowitt, S. J. Clark, E. Tarelli, D. Uhrin, P. N. Barlow, R. B. Sim, A. J. Day, S. M. Lea
Structural Basis For Complement Factor H Linked Age-Related Macular Degeneration.
J. Exp. Med. V. 204 2277 2007
PubMed-ID: 17893204 | Reference-DOI: 10.1084/JEM.20071069

Compounds

Molecule 1 - COMPLEMENT FACTOR H
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-14B
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Fragment	:	DOMAINS 6,7 AND 8, RESIDUES 322-506
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	H FACTOR 1, HUMAN COMPLEMENT FACTOR H

Structural Features

Chains, Units

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (5, 10)

Asymmetric/Biological Unit (5, 10)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
4	SCR	1	Ligand/Ion	SUCROSE OCTASULFATE
5	SO4	3	Ligand/Ion	SULFATE ION

Sites (7, 7)

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	MSE A:320 , HIS A:337 , ARG A:341 , TYR A:352 , TYR A:353 , SER A:354 , HIS A:360 , TRP A:369 , HIS A:371 , TYR A:390 , PHE A:391 , PRO A:392 , TYR A:393 , HIS A:402 , ARG A:444 , GOL A:1513 , HOH A:2039 , HOH A:2040 , HOH A:2041 , HOH A:2042	BINDING SITE FOR RESIDUE SCR A1507
2	AC2	SOFTWARE	GLU A:395 , ASN A:396 , CYS A:442	BINDING SITE FOR RESIDUE CL A1508
3	AC3	SOFTWARE	ASN A:399 , GLN A:400 , ASN A:401 , HIS A:402 , ILE A:455 , GLY A:458	BINDING SITE FOR RESIDUE CL A1509
4	AC4	SOFTWARE	ARG A:404 , PHE A:459 , SO4 A:1512 , HOH A:2043 , HOH A:2044	BINDING SITE FOR RESIDUE SO4 A1510
5	AC5	SOFTWARE	VAL A:407 , LYS A:410 , SO4 A:1512	BINDING SITE FOR RESIDUE SO4 A1511
6	AC6	SOFTWARE	ARG A:404 , GLU A:462 , SER A:463 , SO4 A:1510 , SO4 A:1511 , HOH A:2045	BINDING SITE FOR RESIDUE SO4 A1512
7	AC7	SOFTWARE	TYR A:368 , TRP A:369 , ARG A:444 , SCR A:1507	BINDING SITE FOR RESIDUE GOL A1513

SS Bonds (6, 6)

Asymmetric/Biological Unit

No.	Residues
1	A:325	-	A:374
2	A:357	-	A:385
3	A:389	-	A:431
4	A:416	-	A:442
5	A:448	-	A:494
6	A:477	-	A:505

Cis Peptide Bonds (8, 8)

Asymmetric/Biological Unit

No.	Residues
1	Arg A:342	-	Pro A:343
2	Phe A:345	-	Pro A:346
3	Ser A:380	-	Pro A:381
4	Pro A:423	-	Lys A:424
5	Lys A:424	-	Ala A:425
6	Ser A:437	-	Pro A:438
7	Glu A:462	-	Ser A:463
8	Asp A:485	-	Gly A:486

Sequence-Structure Mapping

SAPs(SNPs)/Variants (5, 5)

Asymmetric/Biological Unit (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_063648	C	325	Y	CFAH_HUMAN	Disease (AHUS1)	---	A	C	325	Y
2	UniProt	VAR_031980	Q	400	K	CFAH_HUMAN	Disease (AHUS1)	---	A	Q	400	K
3	UniProt	VAR_001979	Y	402	H	CFAH_HUMAN	Polymorphism	1061170	A	H	402	H
4	UniProt	VAR_031981	C	431	S	CFAH_HUMAN	Disease (CFHD)	---	A	C	431	S
5	UniProt	VAR_043892	T	493	R	CFAH_HUMAN	Polymorphism	1061171	A	T	493	R

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

PROSITE Motifs (1, 2)

Asymmetric/Biological Unit (1, 2)

	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	2	- - - - - A:387-444 A:446-506 - - - - - - - - - - - -

Exons (4, 4)

Asymmetric/Biological Unit (4, 4)

	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	1	A:320-322	3
1.7	ENST00000367429	7	ENSE00001769047	chr1:196658550-196658744	195	CFAH_HUMAN	322-387	66	1	A:322-387	66
1.8a	ENST00000367429	8a	ENSE00001597868	chr1:196659193-196659369	177	CFAH_HUMAN	387-446	60	1	A:387-446	60
1.12	ENST00000367429	12	ENSE00000469044	chr1:196682865-196683047	183	CFAH_HUMAN	446-507	62	1	A:446-506	61
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	0	-	-
1.17	ENST00000367429	17	ENSE00000791025	chr1:196697476-196697652	177	CFAH_HUMAN	746-805	60	0	-	-
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	-	-

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

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:187
 aligned with CFAH_HUMAN | P08603 from UniProtKB/Swiss-Prot  Length:1231

    Alignment length:187
                                   329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       
           CFAH_HUMAN   320 CTLKPCDYPDIKHGGLYHENMRRPYFPVAVGKYYSYYCDEHFETPSGSYWDHIHCTQDGWSPAVPCLRKCYFPYLENGYNQNYGRKFVQGKSIDVACHPGYALPKAQTTVTCMENGWSPTPRCIRVKTCSKSSIDIENGFISESQYTYALKEKAKYQCKLGYVTADGETSGSITCGKDGWSAQPTCI 506
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------Sushi-2v8eA01 A:448-505                                   - Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------Sushi-2v8eA02 A:448-505                                   - Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------------------------------Sushi-2v8eA03 A:448-505                                   - Pfam domains (3)
         Sec.struct. author .............eee.hhhhhh.........eeeeee...ee......eeeeeee..eee.....eeeee..............eee...eee......ee......eeeee..eee.....ee..eee........ee......eee...eeeeee...........eeeeeee..ee....... Sec.struct. author
                 SAPs(SNPs) -----Y--------------------------------------------------------------------------K-H----------------------------S-------------------------------------------------------------R------------- SAPs(SNPs)
                    PROSITE SUS----------------------------------------------------------------SUSHI  PDB: A:387-444 UniProt: 387-444                    -SUSHI  PDB: A:446-506 UniProt: 446-507                        PROSITE
           Transcript 1 (1) 1.6---------------------------------------------------------------------------------------------------------------------------Exon 1.12  PDB: A:446-506 UniProt: 446-507 [INCOMPLETE]       Transcript 1 (1)
           Transcript 1 (2) --Exon 1.7  PDB: A:322-387 UniProt: 322-387                         ----------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
           Transcript 1 (3) -------------------------------------------------------------------Exon 1.8a  PDB: A:387-446 UniProt: 387-446                  ------------------------------------------------------------ Transcript 1 (3)
                 2v8e A 320 mGLKPCDYPDIKHGGLYHENmRRPYFPVAVGKYYSYYCDEHFETPSGSYWDHIHCTQDGWSPAVPCLRKCYFPYLENGYNQNHGRKFVQGKSIDVACHPGYALPKAQTTVTCmENGWSPTPRCIRVKTCSKSSIDIENGFISESQYTYALKEKAKYQCKLGYVTADGETSGSITCGKDGWSAQPTCI 506
                            |      329       339|      349       359       369       379       389       399       409       419       429  |    439       449       459       469       479       489       499       
                            |                 340-MSE                                                                                     432-MSE                                                                      
                          320-MSE

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

(no "SCOP Domain" information available for 2V8E)

CATH Domains (0, 0)

(no "CATH Domain" information available for 2V8E)

Pfam Domains (1, 3)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Sushi (50)

Homo sapiens (Human) (42)

1a	Sushi-2v8eA01	A:448-505
1b	Sushi-2v8eA02	A:448-505
1c	Sushi-2v8eA03	A:448-505

Gene Ontology (12, 12)

Asymmetric/Biological Unit(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.

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	Cis Peptide Bonds
		Arg A:342 - Pro A:343	[ RasMol ]
		Asp A:485 - Gly A:486	[ RasMol ]
		Glu A:462 - Ser A:463	[ RasMol ]
		Lys A:424 - Ala A:425	[ RasMol ]
		Phe A:345 - Pro A:346	[ RasMol ]
		Pro A:423 - Lys A:424	[ RasMol ]
		Ser A:380 - Pro A:381	[ RasMol ]
		Ser A:437 - Pro A:438	[ RasMol ]

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	2v8e
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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	CFAH_HUMAN \| P08603	:	1fhc 1haq 1hcc 1hfh 1hfi 1kov 2bzm 2g7i 2ic4 2jgw 2jgx 2kms 2qfg 2qfh 2rlp 2rlq 2uwn 2w80 2w81 2wii 2xqw 3gau 3gav 3gaw 3kxv 3kzj 3oxu 3r62 3rj3 3sw0 4ayd 4aye 4ayi 4aym 4b2r 4b2s 4j38 4k12 4ont 4zh1 5o32 5o35

Related Entries Specified in the PDB File

1fhc	C3D AND HEPARIN BINDING COMPLEMENT FACTOR H DOMAINS SCR19-20
1haq	FOUR MODELS OF HUMAN FACTOR H DETERMINED BY SOLUTION SCATTERING CURVE-FITTING AND HOMOLOGY MODELLING
1hcc
1hfh	FACTOR H, 15TH AND 16TH C-MODULE PAIR ( NMR, MINIMIZED AVERAGED STRUCTURE)
1hfi	FACTOR H, 15TH C-MODULE PAIR (NMR, MINIMIZED AVERAGED STRUCTURE)
1kov	HOMOLOGY MODEL OF HUMAN FACTOR H SCRS 6 AND 7
2bzm	SOLUTION STRUCTURE OF THE PRIMARY HOST RECOGNITION REGION OF COMPLEMENT FACTOR H
2g7i	STRUCTURE OF HUMAN COMPLEMENT FACTOR H CARBOXYL TERMINALDOMAINS 19-20: A BASIS FOR ATYPICAL HEMOLYTIC UREMICSYNDROME
2jgw	STRUCTURE OF CCP MODULE 7 OF COMPLEMENT FACTOR H - THE AMD AT RISK VARIENT (402H)
2jgx	STRUCTURE OF CCP MODULE 7 OF COMPLEMENT FACTOR H - THE AMD NOT AT RISK VARIENT ( 402Y)
2uwn	CRYSTAL STRUCTURE OF HUMAN COMPLEMENT FACTOR H, SCR DOMAINS 6-8 (H402 RISK VARIANT), IN COMPLEX WITH LIGAND.