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(-) Description

Title :  SOLUTION STRUCTURE OF CCP MODULES 10-11 OF COMPLEMENT FACTOR H
 
Authors :  E. Makou, H. D. T. Mertens, M. Maciejewski, D. C. Soares, I. Matis, C. Q. S A. P. Herbert, D. I. Svergun, P. N. Barlow
Date :  17 Jul 12  (Deposition) - 10 Oct 12  (Release) - 30 Nov 16  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Immune System, Short Consensus Repeat (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Makou, H. D. T. Mertens, M. Maciejewski, D. C. Soares, I. Matis, C. Q. Schmidt, A. P. Herbert, D. I. Svergun, P. N. Barlow
Solution Structure Of Ccp Modules 10-12 Illuminates Functional Architecture Of The Complement Regulator, Factor H.
J. Mol. Biol. V. 424 295 2012
PubMed-ID: 23017427  |  Reference-DOI: 10.1016/J.JMB.2012.09.013

(-) Compounds

Molecule 1 - COMPLEMENT FACTOR H
    ChainsA
    EngineeredYES
    Expression SystemKOMAGATAELLA PASTORIS
    Expression System PlasmidPPICZAB
    Expression System StrainKM71H
    Expression System Taxid4922
    Expression System Vector TypePLASMID
    FragmentCCPS 10-11, RESIDUES 566-687
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymH FACTOR 1

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4B2R)

(-) Sites  (0, 0)

(no "Site" information available for 4B2R)

(-) SS Bonds  (4, 4)

NMR Structure
No.Residues
1A:569 -A:611
2A:597 -A:623
3A:630 -A:673
4A:659 -A:684

(-) Cis Peptide Bonds  (1, 20)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Ser A:617 -Pro A:618

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 5)

NMR Structure (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_043893R567GCFAH_HUMANUnclassified  ---AR567G
2UniProtVAR_063649V609ICFAH_HUMANDisease (AHUS1)  ---AV609I
3UniProtVAR_025865C630WCFAH_HUMANDisease (AHUS1)  ---AC630W
4UniProtVAR_031982C673SCFAH_HUMANDisease (CFHD)  ---AC673S
5UniProtVAR_031983C673YCFAH_HUMANDisease (AHUS1)  ---AC673Y

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
NMR Structure * (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_043893R567GCFAH_HUMANUnclassified  ---AR567G
2UniProtVAR_063649V609ICFAH_HUMANDisease (AHUS1)  ---AV609I
3UniProtVAR_025865C630WCFAH_HUMANDisease (AHUS1)  ---AC630W
4UniProtVAR_031982C673SCFAH_HUMANDisease (CFHD)  ---AC673S
5UniProtVAR_031983C673YCFAH_HUMANDisease (AHUS1)  ---AC673Y

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

(-) PROSITE Motifs  (1, 3)

NMR Structure (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUSHIPS50923 Sushi/CCP/SCR domain profile.CFAH_HUMAN19-82
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
  3-
-
-
-
-
-
-
A:566-566
A:567-625
A:628-686
-
-
-
-
-
-
-
-
-
NMR Structure * (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUSHIPS50923 Sushi/CCP/SCR domain profile.CFAH_HUMAN19-82
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
  3-
-
-
-
-
-
-
A:566-566
A:567-625
A:628-686
-
-
-
-
-
-
-
-
-

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003674291aENSE00001444484chr1:196621008-196621305298CFAH_HUMAN1-20200--
1.2aENST000003674292aENSE00001134426chr1:196642108-196642293186CFAH_HUMAN20-82630--
1.3ENST000003674293ENSE00000791013chr1:196642987-196643092106CFAH_HUMAN82-117360--
1.4ENST000003674294ENSE00000791014chr1:196645119-19664519577CFAH_HUMAN117-143270--
1.5bENST000003674295bENSE00000469039chr1:196646606-196646797192CFAH_HUMAN143-207650--
1.5cENST000003674295cENSE00000791016chr1:196648753-196648923171CFAH_HUMAN207-264580--
1.6ENST000003674296ENSE00000469041chr1:196654194-196654367174CFAH_HUMAN264-322590--
1.7ENST000003674297ENSE00001769047chr1:196658550-196658744195CFAH_HUMAN322-387660--
1.8aENST000003674298aENSE00001597868chr1:196659193-196659369177CFAH_HUMAN387-446600--
1.12ENST0000036742912ENSE00000469044chr1:196682865-196683047183CFAH_HUMAN446-507621A:562-5654
1.13ENST0000036742913ENSE00000469045chr1:196684723-196684899177CFAH_HUMAN507-566601A:566-5661
1.14ENST0000036742914ENSE00000791022chr1:196694251-196694427177CFAH_HUMAN566-625601A:566-62560
1.15ENST0000036742915ENSE00000791023chr1:196695600-196695782183CFAH_HUMAN625-686621A:625-68662
1.16ENST0000036742916ENSE00000469048chr1:196695891-196696070180CFAH_HUMAN686-746611A:686-6872
1.17ENST0000036742917ENSE00000791025chr1:196697476-196697652177CFAH_HUMAN746-805600--
1.18aENST0000036742918aENSE00000791026chr1:196705954-196706136183CFAH_HUMAN805-866620--
1.19ENST0000036742919ENSE00000791027chr1:196706605-196706790186CFAH_HUMAN866-928630--
1.20aENST0000036742920aENSE00000791028chr1:196709749-196709922174CFAH_HUMAN928-986590--
1.20dENST0000036742920dENSE00000469053chr1:196711005-196711181177CFAH_HUMAN986-1045600--
1.21ENST0000036742921ENSE00001622338chr1:196712582-196712758177CFAH_HUMAN1045-1104600--
1.22ENST0000036742922ENSE00001719380chr1:196714947-196715129183CFAH_HUMAN1104-1165620--
1.23ENST0000036742923ENSE00001931000chr1:196716241-196716634394CFAH_HUMAN1165-1231670--

(-) Sequences/Alignments

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
(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:126
 aligned with CFAH_HUMAN | P08603 from UniProtKB/Swiss-Prot  Length:1231

    Alignment length:201
                                   496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686 
           CFAH_HUMAN   487 ETSGSITCGKDGWSAQPTCIKSCDIPVFMNARTKNDFTWFKLNDTLDYECHDGYESNTGSTTGSIVCGYNGWSDLPICYERECELPKIDVHLVPDRKKDQYKVGEVLKFSCKPGFTIVGPNSVQCYHFGLSPDLPICKEQVQSCGPPPELLNGNVKEKTKEEYGHSEVVEYYCNPRFLMKGPNKIQCVDGEWTTLPVCIVE 687
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....---------------------------------------------------------------------------...ee.......eee.....ee....eeeeee....eee...eeeee..eee....eee...............ee............eeeee....eee....eee...........eee. Sec.struct. author
             SAPs(SNPs) (1) --------------------------------------------------------------------------------G-----------------------------------------I--------------------W------------------------------------------S-------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y-------------- SAPs(SNPs) (2)
                    PROSITE SUSHI  PDB: -        -------SUSHI  PDB: A:566-566 UniProt: 515-566              SUSHI  PDB: A:567-625 UniProt: 567-625                     --SUSHI  PDB: A:628-686 UniProt: 628-686                     - PROSITE
           Transcript 1 (1) Exon 1.12            ----------------------------------------------------------Exon 1.14  PDB: A:566-625 UniProt: 566-625                  ------------------------------------------------------------1. Transcript 1 (1)
           Transcript 1 (2) --------------------Exon 1.13  PDB: A:566-566 UniProt: 507-566 [INCOMPLETE]     ----------------------------------------------------------Exon 1.15  PDB: A:625-686 UniProt: 625-686                    - Transcript 1 (2)
                 4b2r A 562 EAAG---------------------------------------------------------------------------ERECELPKIDVHLVPDRKKDQYKVGEVLKFSCKPGFTIVGPNSVQCYHFGLSPDLPICKEQVQSCGPPPELLNGNVKEKTKEEYGHSEVVEYYCNPRFLMKGPNKIQCVDGEWTTLPVCIVE 687
                               |     -         -         -         -         -         -         -       566       576       586       596       606       616       626       636       646       656       666       676       686 
                             565                                                                         566                                                                                                                         

   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 4B2R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4B2R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B2R)

(-) Gene Ontology  (12, 12)

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.

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  Cis Peptide Bonds
    Ser A:617 - Pro A:618   [ RasMol ]  
 

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CFAH_HUMAN | P086031fhc 1haq 1hcc 1hfh 1hfi 1kov 2bzm 2g7i 2ic4 2jgw 2jgx 2kms 2qfg 2qfh 2rlp 2rlq 2uwn 2v8e 2w80 2w81 2wii 2xqw 3gau 3gav 3gaw 3kxv 3kzj 3oxu 3r62 3rj3 3sw0 4ayd 4aye 4ayi 4aym 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
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.
2v8e CRYSTAL STRUCTURE OF HUMAN COMPLEMENT FACTOR H, SCR DOMAINS 6-8 (H402 RISK VARIANT), IN COMPLEX WITH LIGAND.
2w80 STRUCTURE OF A COMPLEX BETWEEN NEISSERIA MENINGITIDIS FACTOR H BINDING PROTEIN AND CCPS 6-7 OF HUMAN COMPLEMENT FACTOR H
2w81 STRUCTURE OF A COMPLEX BETWEEN NEISSERIA MENINGITIDIS FACTOR H BINDING PROTEIN AND CCPS 6-7 OF HUMAN COMPLEMENT FACTOR H
2wii COMPLEMENT C3B IN COMPLEX WITH FACTOR H DOMAINS 1-4
2xqw STRUCTURE OF FACTOR H DOMAINS 19-20 IN COMPLEX WITH COMPLEMENT C3D
4ayd STRUCTURE OF A COMPLEX BETWEEN CCPS 6 AND 7 OF HUMAN COMPLEMENT FACTOR H AND NEISSERIA MENINGITIDIS FHBP VARIANT 1 R106A MUTANT
4aye STRUCTURE OF A COMPLEX BETWEEN CCPS 6 AND 7 OF HUMAN COMPLEMENT FACTOR H AND NEISSERIA MENINGITIDIS FHBP VARIANT 1 E283AE304A MUTANT
4ayi STRUCTURE OF A COMPLEX BETWEEN CCPS 6 AND 7 OF HUMAN COMPLEMENT FACTOR H AND NEISSERIA MENINGITIDIS FHBP VARIANT 3 WILD TYPE
4aym STRUCTURE OF A COMPLEX BETWEEN CCPS 6 AND 7 OF HUMAN COMPLEMENT FACTOR H AND NEISSERIA MENINGITIDIS FHBP VARIANT 3 P106A MUTANT
4b2s SOLUTION STRUCTURE OF CCP MODULES 11-12 OF COMPLEMENT FACTOR H