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(-) Description

Title :  THE STRUCTURE OF THE TWO N-TERMINAL DOMAINS OF COMPLEMENT FACTOR H RELATED PROTEIN 1 SHOWS FORMATION OF A NOVEL DIMERISATION INTERFACE
 
Authors :  J. J. E. Caesar, E. Goicoechea De Jorge, M. C. Pickering, S. M. Lea
Date :  23 Nov 12  (Deposition) - 13 Mar 13  (Release) - 03 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Immune System, Cfhr-1, Cfhr1, Fhr1 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Goicoechea De Jorge, J. J. E. Caesar, T. H. Malik, M. Patel, M. Colledge, S. Johnson, S. Hakobyan, B. P. Morgan, C. L. Harris, M. C. Pickering, S. M. Lea
Dimerization Of Complement Factor H-Related Proteins Modulates Complement Activation In Vivo.
Proc. Natl. Acad. Sci. Usa V. 110 4685 2013
PubMed-ID: 23487775  |  Reference-DOI: 10.1073/PNAS.1219260110

(-) Compounds

Molecule 1 - COMPLEMENT FACTOR H-RELATED PROTEIN 1
    Chains: A, B
    Engineered: YES
    Expression System: KLUYVEROMYCES LACTIS
    Expression System Strain: GG799
    Expression System Taxid: 28985
    Expression System Vector: PKLAC-2
    Expression System Vector Type: PLASMID
    Fragment: SCR DOMAINS 1 AND 2, RESIDUES 19-143
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: FHR-1, H FACTOR-LIKE PROTEIN 1, H-FACTOR-LIKE 1, H36

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 16)

Asymmetric/Biological Unit (1, 16)
No.NameCountTypeFull Name
1EDO16Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:15 , ASP A:17 , EDO B:1125BINDING SITE FOR RESIDUE EDO A1126
02AC2SOFTWARETYR A:16 , PHE A:33 , TYR A:34 , PRO B:72BINDING SITE FOR RESIDUE EDO A1127
03AC3SOFTWARELEU A:68 , PHE B:48BINDING SITE FOR RESIDUE EDO B1124
04AC4SOFTWAREGLU A:1 , VAL A:74 , GLU A:75 , ASN A:76 , GLY A:77 , HIS A:78 , ASN A:97 , THR B:98BINDING SITE FOR RESIDUE EDO A1128
05AC5SOFTWARETHR A:3 , GLN A:26 , PRO A:28 , SER A:45BINDING SITE FOR RESIDUE EDO A1129
06AC6SOFTWARETRP A:49 , EDO A:1126 , TYR B:39 , ASN B:40 , EDO B:1128BINDING SITE FOR RESIDUE EDO B1125
07AC7SOFTWAREGLY A:83 , THR A:85 , TRP B:49BINDING SITE FOR RESIDUE EDO A1130
08AC8SOFTWARESER B:36 , CYS B:37 , VAL B:42 , SER B:43 , LYS B:46 , SER B:47 , PHE B:48 , HOH B:2012BINDING SITE FOR RESIDUE EDO B1126
09AC9SOFTWARETHR B:50 , ARG B:51BINDING SITE FOR RESIDUE EDO B1127
10BC1SOFTWAREPHE A:48 , TRP A:49 , ASN B:40 , LEU B:68 , CYS B:69 , PHE B:70 , TRP B:116 , EDO B:1125BINDING SITE FOR RESIDUE EDO B1128
11BC2SOFTWAREPRO A:72 , PHE A:73 , TYR B:16 , TYR B:21 , VAL B:32BINDING SITE FOR RESIDUE EDO B1129
12BC3SOFTWAREVAL A:74 , GLU A:75 , LYS A:121 , CYS A:122 , HOH A:2043BINDING SITE FOR RESIDUE EDO A1131
13BC4SOFTWARESER A:36 , CYS A:37 , PHE A:48 , HOH A:2028 , HOH A:2074BINDING SITE FOR RESIDUE EDO A1132
14BC5SOFTWAREARG A:114 , TRP A:116 , SER A:117BINDING SITE FOR RESIDUE EDO A1133
15BC6SOFTWAREGLN A:84 , THR A:85 , ASP A:90 , GLU B:57BINDING SITE FOR RESIDUE EDO A1134
16BC7SOFTWARETHR A:91 , ASN A:108 , SER A:110 , GLU B:88 , VAL B:112 , GLU B:113BINDING SITE FOR RESIDUE EDO B1130

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:5 -A:54
2A:37 -A:65
3A:69 -A:111
4A:96 -A:122
5B:5 -B:54
6B:37 -B:65
7B:69 -B:111
8B:96 -B:122

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ser A:60 -Pro A:61
2Ser B:60 -Pro B:61
3Gln B:103 -Asn B:104

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZD2)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUSHIPS50923 Sushi/CCP/SCR domain profile.FHR1_HUMAN85-142
 
145-203
206-264
273-329		  2A:67-124
B:67-123
-
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 3ZD2)

(-) 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:125
 aligned with FHR1_HUMAN | Q03591 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:125
                                    28        38        48        58        68        78        88        98       108       118       128       138     
           FHR1_HUMAN    19 EATFCDFPKINHGILYDEEKYKPFSQVPTGEVFYYSCEYNFVSPSKSFWTRITCTEEGWSPTPKCLRLCFFPFVENGHSESSGQTHLEGDTVQIICNTGYRLQNNENNISCVERGWSTPPKCRST 143
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee......eee.hhhhh....eee...eeeeee...ee.......eeeeee..eee.....eeee.......ee.......ee...ee..ee............eeee..ee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------SUSHI  PDB: A:67-124 UniProt: 85-142                      - PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zd2 A   1 EATFCDFPKINHGILYDEEKYKPFSQVPTGEVFYYSCEYNFVSPSKSFWTRITCTEEGWSPTPKCLRLCFFPFVENGHSESSGQTHLEGDTVQIICNTGYRLQNNENNISCVERGWSTPPKCRST 125
                                    10        20        30        40        50        60        70        80        90       100       110       120     


Chain B from PDB  Type:PROTEIN  Length:119
 aligned with FHR1_HUMAN | Q03591 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:122
                                    29        39        49        59        69        79        89        99       109       119       129       139  
           FHR1_HUMAN    20 ATFCDFPKINHGILYDEEKYKPFSQVPTGEVFYYSCEYNFVSPSKSFWTRITCTEEGWSPTPKCLRLCFFPFVENGHSESSGQTHLEGDTVQIICNTGYRLQNNENNISCVERGWSTPPKCR 141
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.......eee......---..ee...eeeeee...ee.......eeeeee..eee.....eeeee......ee......eee...eee.ee...........eeeee..ee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------SUSHI  PDB: B:67-123 UniProt: 85-142                      PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zd2 B   2 ATFCDFPKINHGILYDEEKY---SQVPTGEVFYYSCEYNFVSPSKSFWTRITCTEEGWSPTPKCLRLCFFPFVENGHSESSGQTHLEGDTVQIICNTGYRLQNNENNISCVERGWSTPPKCR 123
                                    11        21   |    31        41        51        61        71        81        91       101       111       121  
                                              21  25
   Legend:   → Mismatch (orange background)
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  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 3ZD2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZD2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZD2)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (FHR1_HUMAN | Q03591)
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.
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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 Related Entries

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

UniProtKB/Swiss-Prot
        FHR1_HUMAN | Q03591: 3rj3 4muc

(-) Related Entries Specified in the PDB File

3zd1 STRUCTURE OF THE TWO C-TERMINAL DOMAINS OF COMPLEMENT FACTOR H RELATED PROTEIN 2