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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CYP7A1 IN COMPLEX WITH CHOLEST-4-EN-3-ONE
 
Authors :  N. Strushkevich, W. Tempel, F. Mackenzie, A. K. Wernimont, C. H. Arrows A. M. Edwards, C. Bountra, J. Weigelt, H. Park, Structural Genomics Consortium (Sgc)
Date :  28 Jun 11  (Deposition) - 13 Jul 11  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Cytochrome P450, Cholesterol 7-Alpha Hydroxylase, Cyp7A1, Cholest-4- En-3-One, Bile Acid Biosynthesis, Structural Genomics, Structural Genomics Consortium, Sgc, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Strushkevich, W. Tempel, F. Mackenzie, A. K. Wernimont, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, H. Park
Crystal Structure Of Human Cyp7A1 In Complex With Cholest-4-En-3-One
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CHOLESTEROL 7-ALPHA-MONOOXYGENASE
    ChainsA, B
    EC Number1.14.13.17
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPCW-LIC-29
    Expression System StrainJM109
    Expression System Taxid562
    FragmentUNP RESIDUES 25-503
    GeneCYP7A1, CYP7
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCYP7A1, CYPVII, CHOLESTEROL 7-ALPHA-HYDROXYLASE, CYTOCHROME P450 7A1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2K2B2Ligand/Ion(8ALPHA,9BETA)-CHOLEST-4-EN-3-ONE
3UNX8Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2K2B1Ligand/Ion(8ALPHA,9BETA)-CHOLEST-4-EN-3-ONE
3UNX4Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2K2B1Ligand/Ion(8ALPHA,9BETA)-CHOLEST-4-EN-3-ONE
3UNX4Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:101 , PHE A:129 , ALA A:285 , SER A:286 , ASN A:289 , THR A:290 , ALA A:293 , SER A:360 , ASN A:362 , PRO A:436 , PHE A:437 , THR A:442 , CYS A:444 , PRO A:445 , ALA A:450 , GLU A:453 , K2B A:1429 , HOH A:2601BINDING SITE FOR RESIDUE HEM A 601
2AC2SOFTWAREHIS A:101 , LEU A:104 , SER A:105 , ILE A:114 , ILE A:125 , ARG A:260 , VAL A:281 , ALA A:285 , SER A:360 , LEU A:361 , GLY A:485 , LEU A:486 , HEM A:601BINDING SITE FOR RESIDUE K2B A 1429
3AC3SOFTWAREHIS B:101 , PHE B:129 , ALA B:285 , SER B:286 , ASN B:289 , THR B:290 , ALA B:293 , SER B:360 , ASN B:362 , PRO B:436 , PHE B:437 , THR B:442 , CYS B:444 , PRO B:445 , ALA B:450 , GLU B:453 , K2B B:1429 , HOH B:2601BINDING SITE FOR RESIDUE HEM B 601
4AC4SOFTWAREHIS B:101 , LEU B:104 , SER B:105 , ILE B:114 , ILE B:125 , ARG B:260 , VAL B:281 , ALA B:285 , SER B:360 , LEU B:361 , GLY B:485 , LEU B:486 , HEM B:601BINDING SITE FOR RESIDUE K2B B 1429

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3SN5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3SN5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 8)

Asymmetric Unit (4, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_059152H86NCP7A1_HUMANPolymorphism62621283A/BH86N
2UniProtVAR_001259F100SCP7A1_HUMANPolymorphism  ---A/BF100S
3UniProtVAR_018376N233SCP7A1_HUMANPolymorphism8192874A/BN233S
4UniProtVAR_018377D347NCP7A1_HUMANPolymorphism8192875A/BD347N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_059152H86NCP7A1_HUMANPolymorphism62621283AH86N
2UniProtVAR_001259F100SCP7A1_HUMANPolymorphism  ---AF100S
3UniProtVAR_018376N233SCP7A1_HUMANPolymorphism8192874AN233S
4UniProtVAR_018377D347NCP7A1_HUMANPolymorphism8192875AD347N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_059152H86NCP7A1_HUMANPolymorphism62621283BH86N
2UniProtVAR_001259F100SCP7A1_HUMANPolymorphism  ---BF100S
3UniProtVAR_018376N233SCP7A1_HUMANPolymorphism8192874BN233S
4UniProtVAR_018377D347NCP7A1_HUMANPolymorphism8192875BD347N

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOCHROME_P450PS00086 Cytochrome P450 cysteine heme-iron ligand signature.CP7A1_HUMAN437-446
 
  2A:437-446
B:437-446
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOCHROME_P450PS00086 Cytochrome P450 cysteine heme-iron ligand signature.CP7A1_HUMAN437-446
 
  1A:437-446
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOCHROME_P450PS00086 Cytochrome P450 cysteine heme-iron ligand signature.CP7A1_HUMAN437-446
 
  1-
B:437-446

(-) Exons   (0, 0)

(no "Exon" information available for 3SN5)

(-) 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:468
 aligned with CP7A1_HUMAN | P22680 from UniProtKB/Swiss-Prot  Length:504

    Alignment length:480
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       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       453       463       473       483       493       503
          CP7A1_HUMAN    24 IRRRQTGEPPLENGLIPYLGCALQFGANPLEFLRANQRKHGHVFTCKLMGKYVHFITNPLSYHKVLCHGKYFDWKKFHFATSAKAFGHRSIDPMDGNTTENINDTFIKTLQGHALNSLTESMMENLQRIMRPPVSSNSKTAAWVTEGMYSFCYRVMFEAGYLTIFGRDLTRRDTQKAHILNNLDNFKQFDKVFPALVAGLPIHMFRTAHNAREKLAESLRHENLQKRESISELISLRMFLNDTLSTFDDLEKAKTHLVVLWASQANTIPATFWSLFQMIRNPEAMKAATEEVKRTLENAGQKVSLEGNPICLSQAELNDLPVLDSIIKESLRLSSASLNIRTAKEDFTLHLEDGSYNIRKDDIIALYPQLMHLDPEIYPDPLTFKYDRYLDENGKTKTTFYCNGLKLKYYYMPFGSGATICPGRLFAIHEIKQFLILMLSYFELELIEGQAKCPPLDQSRAGLGILPPLNDIEFKYKFKH 503
               SCOP domains d3sn5a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........ee........hhhhhhhhhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhhh....ee.hhhhhhhhhhhhh....hhhhh....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh--------....eeeehhhhhhhhhhhhhhhhhhh....----hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhheee.eeeee...eeee....eeee....eeee.hhhhhh...........................ee..ee........ee..ee..hhhhhhhhhhhhhhhhhhheeeee..........hhhhh.eee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------N-------------S------------------------------------------------------------------------------------------------------------------------------------S-----------------------------------------------------------------------------------------------------------------N------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME--------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3sn5 A  24 SRRRQTGEPPLENGLIPYLGCALQFGANPLEFLRANQRKHGHVFTCKLMGKYVHFITNPLSYHKVLCHGKYFDWKKFHFALSAKAFGHRSIDPMDGNTTENINDTFIKTLQGHALNSLTESMMENLQRIMR--------TAAWVTEGMYSFCYRVMFEAGYLTIFGRDLT----QKAHILNNLDNFKQFDKVFPALVAGLPIHMFRTAHNAREKLAESLRHENLQKRESISELISLRMFLNDTLSTFDDLEKAKTHLVVLWASQANTIPATFWSLFQMIRNPEAMKAATEEVKRTLENAGQKVSLEGNPICLSQAELNDLPVLDSIIKESLRLSSASLNIRTAKEDFTLHLEDGSYNIRKDDIIALYPQLMHLDPEIYPDPLTFKYDRYLDENGKTKTTFYCNGLKLKYYYMPFGSGATICPGRLFAIHEIKQFLILMLSYFELELIEGQAKCPPLDQSRAGLGILPPLNDIEFKYKFKH 503
                                    33        43        53        63        73        83        93       103       113       123       133       143       153|      163       173       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       453       463       473       483       493       503
                                                                                                                                                            154      163                           193  198                                                                                                                                                                                                                                                                                                                 

Chain B from PDB  Type:PROTEIN  Length:466
 aligned with CP7A1_HUMAN | P22680 from UniProtKB/Swiss-Prot  Length:504

    Alignment length:479
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494         
          CP7A1_HUMAN    25 RRRQTGEPPLENGLIPYLGCALQFGANPLEFLRANQRKHGHVFTCKLMGKYVHFITNPLSYHKVLCHGKYFDWKKFHFATSAKAFGHRSIDPMDGNTTENINDTFIKTLQGHALNSLTESMMENLQRIMRPPVSSNSKTAAWVTEGMYSFCYRVMFEAGYLTIFGRDLTRRDTQKAHILNNLDNFKQFDKVFPALVAGLPIHMFRTAHNAREKLAESLRHENLQKRESISELISLRMFLNDTLSTFDDLEKAKTHLVVLWASQANTIPATFWSLFQMIRNPEAMKAATEEVKRTLENAGQKVSLEGNPICLSQAELNDLPVLDSIIKESLRLSSASLNIRTAKEDFTLHLEDGSYNIRKDDIIALYPQLMHLDPEIYPDPLTFKYDRYLDENGKTKTTFYCNGLKLKYYYMPFGSGATICPGRLFAIHEIKQFLILMLSYFELELIEGQAKCPPLDQSRAGLGILPPLNDIEFKYKFKH 503
               SCOP domains d3sn5b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........ee........hhhhhhhhhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhhh....ee.hhhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh----------..eeeehhhhhhhhhhhhhhhhhhhee.....hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.ee..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhh.hhhhhhhhhhhhhhheee.eeeee...eeee....eeee....eeee.hhhhhh...........................ee..ee........ee..ee..hhhhhhhhhhhhhhhhhhheeeee.---......hhhhh.eee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------N-------------S------------------------------------------------------------------------------------------------------------------------------------S-----------------------------------------------------------------------------------------------------------------N------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME--------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sn5 B  25 RRRQTGEPPLENGLIPYLGCALQFGANPLEFLRANQRKHGHVFTCKLMGKYVHFITNPLSYHKVLCHGKYFDWKKFHFALSAKAFGHRSIDPMDGNTTENINDTFIKTLQGHALNSLTESMMENLQRIMR----------AWVTEGMYSFCYRVMFEAGYLTIFGRDLTRRDTQKAHILNNLDNFKQFDKVFPALVAGLPIHMFRTAHNAREKLAESLRHENLQKRESISELISLRMFLNDTLSTFDDLEKAKTHLVVLWASQANTIPATFWSLFQMIRNPEAMKAATEEVKRTLENAGQKVSLEGNPICLSQAELNDLPVLDSIIKESLRLSSASLNIRTAKEDFTLHLEDGSYNIRKDDIIALYPQLMHLDPEIYPDPLTFKYDRYLDENGKTKTTFYCNGLKLKYYYMPFGSGATICPGRLFAIHEIKQFLILMLSYFELELI---AKCPPLDQSRAGLGILPPLNDIEFKYKFKH 503
                                    34        44        54        64        74        84        94       104       114       124       134       144       154         -|      174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464     | 474       484       494         
                                                                                                                                                           154        165                                                                                                                                                                                                                                                                                                              470 474                             

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3SN5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SN5)

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CP7A1_HUMAN | P22680)
molecular function
    GO:0008123    cholesterol 7-alpha-monooxygenase activity    Catalysis of the reaction: cholesterol + NADPH + H+ + O2 = 7-alpha-hydroxycholesterol + NADP+ + H2O.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004497    monooxygenase activity    Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016705    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor.
biological process
    GO:0006699    bile acid biosynthetic process    The chemical reactions and pathways resulting in the formation of bile acids, any of a group of steroid carboxylic acids occurring in bile.
    GO:0071397    cellular response to cholesterol    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cholesterol stimulus.
    GO:0071333    cellular response to glucose stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucose stimulus.
    GO:0006707    cholesterol catabolic process    The chemical reactions and pathways resulting in the breakdown of cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones.
    GO:0042632    cholesterol homeostasis    Any process involved in the maintenance of an internal steady state of cholesterol within an organism or cell.
    GO:0008203    cholesterol metabolic process    The chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. It is a component of the plasma membrane lipid bilayer and of plasma lipoproteins and can be found in all animal tissues.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0070857    regulation of bile acid biosynthetic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of bile acids.
    GO:0008202    steroid metabolic process    The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
    GO:0016125    sterol metabolic process    The chemical reactions and pathways involving sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule.
cellular component
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0031090    organelle membrane    A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CP7A1_HUMAN | P226803dax 3v8d

(-) Related Entries Specified in the PDB File

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