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(-) Description

Title :  AN ANTIBODY AGAINST THE C-TERMINAL DOMAIN OF PCSK9 LOWERS LDL CHOLESTEROL LEVELS IN VIVO
 
Authors :  F. Schiele, H. Nar
Date :  18 Apr 13  (Deposition) - 08 May 13  (Release) - 19 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.22
Chains :  Asym. Unit :  A,B,C,D,H,L
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  H,L  (1x)
Keywords :  Immunoglobulin, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Schiele, J. Park, N. Redemann, G. Luippold, H. Nar
An Antibody Against The C-Terminal Domain Of Pcsk9 Lowers Ldl Cholesterol Levels In Vivo.
J. Mol. Biol. V. 426 843 2014
PubMed-ID: 24252255  |  Reference-DOI: 10.1016/J.JMB.2013.11.011

(-) Compounds

Molecule 1 - PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9
    Chains: A
    EC Number: 3.4.21.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 61-152
    Gene: NARC1, PCSK9, PSEC0052
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NEURAL APOPTOSIS-REGULATED CONVERTASE 1, NARC-1, PROPROTEIN CONVERTASE 9, PC9, SUBTILISIN/KEXIN-LIKE PROTEASE PC9
 
Molecule 2 - PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9
    Chains: B
    EC Number: 3.4.21.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 153-692
    Gene: NARC1, PCSK9, PSEC0052
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NEURAL APOPTOSIS-REGULATED CONVERTASE 1, NARC-1, PROPROTEIN CONVERTASE 9, PC9, SUBTILISIN/KEXIN-LIKE PROTEASE PC9
 
Molecule 3 - FAB1, LIGHT CHAIN
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 4 - FAB1, HEAVY CHAIN
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 5 - FAB3H42, LIGHT CHAIN
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 6 - FAB3H42, HEAVY CHAIN
    Chains: L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDHL
Biological Unit 1 (1x): AB    
Biological Unit 2 (1x):   CD  
Biological Unit 3 (1x):     HL

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4K8R)

(-) Sites  (0, 0)

(no "Site" information available for 4K8R)

(-) SS Bonds  (17, 17)

Asymmetric Unit
No.Residues
1B:223 -B:255
2B:323 -B:358
3B:375 -B:378
4B:457 -B:527
5B:477 -B:526
6B:486 -B:509
7B:534 -B:601
8B:552 -B:600
9B:562 -B:588
10B:608 -B:679
11B:626 -B:678
12B:635 -B:654
13C:24 -C:89
14H:22 -H:96
15H:150 -H:206
16L:22 -L:90
17L:139 -L:198

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Ser B:326 -Pro B:327
2Ser C:8 -Pro C:9
3Tyr C:141 -Pro C:142
4Gly D:106 -Ser D:107
5Ser D:107 -Asp D:108
6Phe D:161 -Pro D:162
7Glu D:163 -Pro D:164
8Phe H:156 -Pro H:157
9Glu H:158 -Pro H:159
10Tyr L:145 -Pro L:146

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K8R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K8R)

(-) Exons   (0, 0)

(no "Exon" information available for 4K8R)

(-) 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:92
                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...hhh.eeeeeeeeee....hhhhhhhhhhhhhhhhhhh....eeeeee.....eeeee.hhhhhhhhhh...eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 4k8r A  61 TATFHRCAKDPWRLPGTYVVVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLPGFLVKMSGDLLELALKLPHVDYIEEDSSVFAQ 152
                                    70        80        90       100       110       120       130       140       150  


Chain B from PDB  Type:PROTEIN  Length:492
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhh.......eeeeee.............eeeeeee.....hhhhh.......hhhhhhhhhhhh..........eeeeee......eeehhhhhhhhhhhhhhhhhh....eeeee.eeee.hhhhhhhhhhhhhh..eeeee......hhh.ee.......eeeeee.......ee..ee........eeee...eeee.......eeee.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhee...hhhhhhhhhhh....ee...........eeeeee..........eeee......eeeeeeee.....eeeeeeee....eeeeeee.......eeeeeeee....eeeeeee........eeee......eeeeeeee........eeee....eeeeeeee...eeeeeeeeee.....eeeee.....eeeeeee........eeeee..eeeee...eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4k8r B 153 SIPWNLERITPPRYYLVEVYLLDTSIQSDHREIEGRVMVTDFENVPEEDGTRFHRQASKCDSHGTHLAGVVSGRDAGVAKGASMRSLRVLNCQGKGTVSGTLIGLEFIRKSQLVQPVGPLVVLLPLAGGYSRVLNAACQRLARAGVVLVTAAGNFRDDACLYSPASAPEVITVGATNAQDQPVTLGTLGTNFGRCVDLFAPGEDIIGASSDCSTCFVSQSGTSQAAAHVAGIAAMMLSAEPELTLAELRQRLIHFSAKDVINEAWFPEDQRVLTPNLVAALPPSTHWQLFCRTVWSAHSGPTRMATAIARCAPDEELLSCSSFSRSGKRRGERMEAQGGKLVCRAHNAFGGEGVYAIARCCLLPQANCSVHTAPPAEASMGTRVHCHQQGHVLTGCSSHWEVEDLPNQCVGHREASIHASCCHAPGLECKVKEHGIPAPQEQVTVACEEGWTLTGCSALPGTSHVLGAYAVDNTCVVRSRAVTAVAICCRSR 682
                                   162   ||| 183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443     ||456       466       476       486       496       506       516       526       536       546       556       566    || 589       599       609       619       629       639       649       659|      680  
                                       166||                                                                                                                                                                                                                                                                           449|                                                                                                                   571|                                                                       659|           
                                        171|                                                                                                                                                                                                                                                                            453                                                                                                                    585                                                                        671           
                                         179                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            


Chain C from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.......eeeee.......eeeeee.......eeee...ee.......eeeee...eeeeee...hhhhh.eeeeee...........eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee........eeeee.........eeeeeeeeeehhhhh....eeeeee.......eeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k8r C   2 AIQLTQSPSSLSASVGDRVTITCRASQGISSALAWYQQKPGKAPKLLIYDASSLESGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQFNSYLITFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 214
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211   


Chain D from PDB  Type:PROTEIN  Length:229
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.......eeeeeee.....eeeeeee.....ee........eeeeee....eeeeee...hhhhheeeeeeeeeeeeee....eeeeee.......eeeee........eeeee...........eeeeeeeeee.................eeeeeeee.....eeeeeeeeehhhhh........eee....eee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k8r D   1 EVQLVESGGGLVQPGGSLRLSCAASGFTFSSYDMHWVRQATGKGLEWVSAIGTAGDTYYPDSVKGRFTISRENAKNSLYLQMNSLRAGDTAVYYCVREGTYYHDSGSDNYYSYGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPS 229
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220         


Chain H from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhh.eeeeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeeee...........ee...eeeee........eeeee.......eeeeeeeeeee.....eeee........eee...ee.....eeeeeeeeee........eeeeeeehhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k8r H   1 EVQLVESGGGLVKPGGSLRLSCAASGFTFSSYSMNWVRQAPGKGLEWVSSISSSSSYISYADSVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYFCARDYDFWSAYYDAFDVWGQGTMVTVSSASTKGPSVFPLAPSSKGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 224
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       143       153       163       173       183       193       203       213       223 
                                                                                                                                                                    139|                                                                                 
                                                                                                                                                                     143                                                                                 


Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee....eeeeeee............eeeee......eeee.............eeeeee..eeeeeee..hhhhh.eeeeeeee....eeee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k8r L   1 ESVLTQPPSVSGAPGQRVTISCTGSSSNIGAGYDVHWYQQLPGTAPKLLISGNSNRPSGVPDRFSGSKSGTSASLAITGLQAEDEADYYCQSYDSSLSGSVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT 214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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 4K8R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K8R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K8R)

(-) Gene Ontology  (61, 61)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu D:163 - Pro D:164   [ RasMol ]  
    Glu H:158 - Pro H:159   [ RasMol ]  
    Gly D:106 - Ser D:107   [ RasMol ]  
    Phe D:161 - Pro D:162   [ RasMol ]  
    Phe H:156 - Pro H:157   [ RasMol ]  
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    Ser C:8 - Pro C:9   [ RasMol ]  
    Ser D:107 - Asp D:108   [ RasMol ]  
    Tyr C:141 - Pro C:142   [ RasMol ]  
    Tyr L:145 - Pro L:146   [ RasMol ]  
 
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  4k8r
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  PCSK9_HUMAN | Q8NBP7
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  3.4.21.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        PCSK9_HUMAN | Q8NBP7: 2p4e 2pmw 2qtw 2w2m 2w2n 2w2o 2w2p 2w2q 2xtj 3bps 3gcw 3gcx 3h42 3m0c 3p5b 3p5c 3sqo 4ne9 4nmx 4ov6

(-) Related Entries Specified in the PDB File

4lkc