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(-) Description

Title :  THE CIDRA DOMAIN FROM HB3VAR03 PFEMP1 BOUND TO ENDOTHELIAL PROTEIN C RECEPTOR
 
Authors :  C. K. Y. Lau, L. Turner, J. S. Jespersen, E. D. Lowe, B. Petersen, C. W. Wan J. E. V. Petersen, J. Lusingu, T. G. Theander, T. Lavstsen, M. K. Higgin
Date :  17 Oct 14  (Deposition) - 17 Dec 14  (Release) - 28 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  C,D  (1x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Signaling Protein, Pfemp1, Epcr, Malaria, Cidr Domain, Endothelial Protein C Receptor, (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. K. Y. Lau, L. Turner, J. S. Jespersen, E. D. Lowe, B. Petersen, C. W. Wang, J. E. V. Petersen, J. Lusingu, T. G. Theander, T. Lavstsen, M. K. Higgins
Structural Conservation Despite Huge Sequence Diversity Allows Epcr Binding By The Pfemp1 Family Implicated In Severe Childhood Malaria.
Cell Host Microbe. V. 17 118 2015
PubMed-ID: 25482433  |  Reference-DOI: 10.1016/J.CHOM.2014.11.007

(-) Compounds

Molecule 1 - HB3VAR03 CIDRA DOMAIN
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI B
    Expression System Plasmid: PET15B
    Expression System Strain: B834
    Expression System Taxid: 37762
    Expression System Vector Type: PLASMID
    Fragment: CIDRA
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 137071
    Strain: HB3
 
Molecule 2 - ENDOTHELIAL PROTEIN C RECEPTOR
    Chains: B, D
    Engineered: YES
    Expression System: DROSOPHILA MELANOGASTER
    Expression System Cell Line: S2
    Expression System Common: FRUIT FLY
    Expression System Plasmid: PEXPRES2-1
    Expression System Taxid: 7227
    Fragment: EXTRACELLULAR DOMAIN, UNP RESIDUES 468-718
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x):   CD
Biological Unit 2 (1x): AB  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 17)

Asymmetric Unit (3, 17)
No.NameCountTypeFull Name
1MAN2Ligand/IonALPHA-D-MANNOSE
2NAG13Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PTY2Ligand/IonPHOSPHATIDYLETHANOLAMINE
Biological Unit 1 (3, 9)
No.NameCountTypeFull Name
1MAN1Ligand/IonALPHA-D-MANNOSE
2NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PTY1Ligand/IonPHOSPHATIDYLETHANOLAMINE
Biological Unit 2 (3, 8)
No.NameCountTypeFull Name
1MAN1Ligand/IonALPHA-D-MANNOSE
2NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PTY1Ligand/IonPHOSPHATIDYLETHANOLAMINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU B:14 , ASN B:30 , HIS B:39 , GLN B:57 , THR B:65 , LEU B:69 , TYR B:72 , GLN B:75 , VAL B:116 , THR B:157 , GLU B:160 , LEU B:161 , PHE B:164 , THR B:168 , TYR B:172BINDING SITE FOR RESIDUE PTY B 200
02AC2SOFTWAREPHE C:656 , LEU D:14 , ASN D:30 , HIS D:39 , GLN D:57 , THR D:65 , LEU D:69 , TYR D:72 , GLN D:75 , PHE D:76 , ARG D:156 , THR D:157 , GLU D:160 , LEU D:161 , THR D:168 , TYR D:172BINDING SITE FOR RESIDUE PTY D 200
03AC3SOFTWAREILE B:16 , ASN B:30 , HIS D:36BINDING SITE FOR MONO-SACCHARIDE NAG B 205 BOUND TO ASN B 30
04AC4SOFTWAREASN B:47 , THR B:49 , ILE D:51 , NAG D:201BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B 201 THROUGH NAG B 202 BOUND TO ASN B 47
05AC5SOFTWARECYS A:526 , THR A:527 , GLU A:529 , ASN A:530 , ASN A:531 , VAL A:613 , ALA B:90 , PHE B:91 , PRO B:92 , ASN B:119 , THR B:140BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B 203 THROUGH MAN B 207 BOUND TO ASN B 119
06AC6SOFTWAREASN B:155BINDING SITE FOR MONO-SACCHARIDE NAG B 206 BOUND TO ASN B 155
07AC7SOFTWAREHIS B:36 , LEU B:37 , GLN B:54 , LEU D:14 , ASN D:30 , SER D:32BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG D 204 THROUGH NAG D 205 BOUND TO ASN D 30
08AC8SOFTWARETHR B:49 , GLN B:66 , NAG B:202 , ASN D:47 , THR D:49BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG D 201 THROUGH NAG D 202 BOUND TO ASN D 47
09AC9SOFTWARETHR C:715 , ALA D:90 , PRO D:92 , LEU D:93 , ASN D:119 , GLN D:138BINDING SITE FOR POLY-SACCHARIDE RESIDUES MAN D 203 THROUGH NAG D 207 BOUND TO ASN D 119
10BC1SOFTWAREASN D:155BINDING SITE FOR MONO-SACCHARIDE NAG D 208 BOUND TO ASN D 155

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:526 -A:614
2A:542 -A:553
3A:596 -A:608
4A:612 -A:710
5B:101 -B:169
6C:526 -C:614
7C:542 -C:553
8C:596 -C:608
9C:612 -C:710
10D:101 -D:169

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe B:91 -Pro B:92
2Phe D:91 -Pro D:92

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4V3D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4V3D)

(-) Exons   (0, 0)

(no "Exon" information available for 4V3D)

(-) Sequences/Alignments

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:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeee.......hhhhhhhhhhh.........eeeeeeee.......eeeeeee........eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4v3d A 499 GDAKNTEINVINSGDKEGYIFEKLSEFCTNENNENGKNYEQWKCYYDNKKNNNKCKMEINIANSKLKNKVTSFDEFFDFWVRKLLIDTIKWETELTYCINNTDVTDCNKCNKNCVCFDKWVKQKEDEWTNIMKLFTNKHDIPKKYYLNINDLFDSFFFQVIYKFNEGEAKWNELKENLKKQIASSSEAAIKVLFNHIKEIATICKDNNTN 716
                                   508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678    || 696       706       716
                                                                                                                                                                                                                  683|                        
                                                                                                                                                                                                                   692                        


Chain B from PDB  Type:PROTEIN  Length:169
                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee..eeeeeeeeee..eeeeeeeee....eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeee........eeeeeeee..eeeeeee....eeee.....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4v3d B   9 QRLHMLQISYFRDPYHVWYQGNASLGGHLTHVLEGPDTNTTIIQLQPLQEPESWARTQSGLQSYLLQFHGLVRLVHQERTLAFPLTIRCFLGCELPPEGSRAHVFFEVAVNGSSFVSFRPERALWQADTQVTSGVVTFTLQQLNAYNRTRYELREFLEDTCVQYVQKHI 177
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168         


Chain C from PDB  Type:PROTEIN  Length:186
                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee.........hhhhhhhhhhh....eeee.........eeeee....eeehhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4v3d C 503 NTEINVINSGDKEGYIFEKLSEFCTNNYEQWKCYYDNKKNNNKCKMEIKNKVTSFDEFFDFWVRKLLIDTIKWETELTYCICNKCNKNCVCFDKWVKQKEDEWTNIMKLFTNKHDIPKKYYLNINDLFDSFFFQVIYKFNEGEAKWNELKENLKKQIASSKSEAAIKVLFNHIKEIATICKDNNTN 716
                                   512       522     ||539       549       566       576       586       596||     613       623       633       643       653       663       673       683||     700       710      
                                                   528|                  557|                             597|                                                                            684|                        
                                                    536                   565                              605                                                                             692                        


Chain D from PDB  Type:PROTEIN  Length:168
                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeeee..eeeeeeeeee..eeeeeeeee....eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeee........eeeeeeee..eeeeeee....eeee.....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4v3d D   9 QRLHMLQISYFRDPYHVWYQGNASLGGHLTHVLEGPDTNTTIIQLQPLQEPESWARTQSGLQSYLLQFHGLVRLVHQERTLAFPLTIRCFLGCELPPEGSRAHVFFEVAVNGSSFVSFRPERALWQADTQVTSGVVTFTLQQLNAYNRTRYELREFLEDTCVQYVQKH 176
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168
   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 4V3D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4V3D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4V3D)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)

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        EPCR_HUMAN | Q9UNN8: 1l8j 1lqv 3jtc 4v3e

(-) Related Entries Specified in the PDB File

4v3e THE CIDRA DOMAIN FROM IT4VAR07 PFEMP1 BOUND TO ENDOTHELIAL PROTEIN C RECEPTOR