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(-) Description

Title :  CRYSTAL STRUCTURE OF BOVINE NPC2 AND CHOLESTEROL SULFATE COMPLEX
 
Authors :  S. Xu, L. Gu, B. Benoff, A. M. Stock
Date :  03 Jul 06  (Deposition) - 26 Jun 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Beta Barrel, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Xu, B. Benoff, H. -L. Liou, P. Lobel, A. M. Stock
Structural Basis Of Sterol Binding By Npc2, A Lysosomal Protein Deficient In Niemann-Pick Type C2 Disease
J. Biol. Chem. V. 282 23525 2007
PubMed-ID: 17573352  |  Reference-DOI: 10.1074/JBC.M703848200

(-) Compounds

Molecule 1 - EPIDIDYMAL SECRETORY PROTEIN E1
    Chains: A, B, C
    Organism Common: CATTLE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Secretion: MILK
    Synonym: NIEMANN PICK TYPE C2 PROTEIN HOMOLOG, NPC2, EPV20

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 16)

Asymmetric Unit (5, 16)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2C3S2Ligand/IonCHOLEST-5-EN-3-YL HYDROGEN SULFATE
3GOL2Ligand/IonGLYCEROL
4NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SO43Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2C3S-1Ligand/IonCHOLEST-5-EN-3-YL HYDROGEN SULFATE
3GOL-1Ligand/IonGLYCEROL
4NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (5, 8)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2C3S1Ligand/IonCHOLEST-5-EN-3-YL HYDROGEN SULFATE
3GOL1Ligand/IonGLYCEROL
4NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SO42Ligand/IonSULFATE ION
Biological Unit 3 (5, 5)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2C3S1Ligand/IonCHOLEST-5-EN-3-YL HYDROGEN SULFATE
3GOL1Ligand/IonGLYCEROL
4NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SO41Ligand/IonSULFATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:39 , HOH A:549 , HOH A:567 , HOH A:579 , HOH A:588BINDING SITE FOR RESIDUE NAG A 402
02AC2SOFTWAREASN B:39 , ASN B:89 , HOH B:776 , VAL C:64 , C3S C:401BINDING SITE FOR RESIDUE NAG B 402
03AC3SOFTWAREASN C:39 , THR C:41 , HOH C:731 , HOH C:753 , HOH C:762BINDING SITE FOR RESIDUE NAG C 402
04AC4SOFTWAREGLU C:1 , ASN C:19 , SER C:21BINDING SITE FOR RESIDUE ACT C 501
05AC5SOFTWAREGLU A:1 , ASN A:19BINDING SITE FOR RESIDUE ACT A 502
06AC6SOFTWAREILE A:68 , LYS A:97BINDING SITE FOR RESIDUE ACT A 503
07AC7SOFTWARESER A:35 , PRO B:22 , HIS B:31 , GLN B:34 , TYR B:36 , HOH B:716 , HOH B:790 , HOH B:791BINDING SITE FOR RESIDUE ACT B 504
08AC8SOFTWARETHR B:25 , LYS B:29 , HIS B:31 , HOH B:724 , HOH B:790BINDING SITE FOR RESIDUE ACT B 505
09AC9SOFTWAREPHE B:66 , PRO B:67 , LYS B:97 , HOH B:749 , HOH B:764 , HOH B:824BINDING SITE FOR RESIDUE ACT B 506
10BC1SOFTWAREGLU B:1 , PRO B:2 , ASN B:19 , HOH B:817 , GLN C:47 , HOH C:782BINDING SITE FOR RESIDUE SO4 B 701
11BC2SOFTWARESER B:102 , ASN B:116 , ALA B:130 , HOH B:734 , HOH B:789BINDING SITE FOR RESIDUE SO4 B 702
12BC3SOFTWARESER A:102 , GLU A:129 , ALA A:130 , LYS C:6BINDING SITE FOR RESIDUE SO4 C 703
13BC4SOFTWAREPRO A:63 , PRO A:65 , HOH A:573 , HOH A:593 , TRP B:11 , PHE B:66 , LEU B:94 , TYR B:100 , PRO B:101 , ILE B:124BINDING SITE FOR RESIDUE C3S B 400
14BC5SOFTWARENAG B:402 , HOH B:796 , VAL C:20 , TYR C:36 , VAL C:38 , LEU C:94 , TYR C:100BINDING SITE FOR RESIDUE C3S C 401
15BC6SOFTWARELYS B:97 , ASN B:98 , GLU B:99 , HOH B:751 , HOH B:781BINDING SITE FOR RESIDUE GOL B 601
16BC7SOFTWARELYS C:97 , ASN C:98 , GLU C:99BINDING SITE FOR RESIDUE GOL C 602

(-) SS Bonds  (9, 9)

Asymmetric Unit
No.Residues
1A:8 -A:121
2A:23 -A:28
3A:74 -A:80
4B:8 -B:121
5B:23 -B:28
6B:74 -B:80
7C:8 -C:121
8C:23 -C:28
9C:74 -C:80

(-) Cis Peptide Bonds  (9, 9)

Asymmetric Unit
No.Residues
1Ser A:21 -Pro A:22
2Gln A:26 -Pro A:27
3Cys A:80 -Pro A:81
4Ser B:21 -Pro B:22
5Gln B:26 -Pro B:27
6Cys B:80 -Pro B:81
7Ser C:21 -Pro C:22
8Gln C:26 -Pro C:27
9Cys C:80 -Pro C:81

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2HKA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2HKA)

(-) Exons   (4, 12)

Asymmetric Unit (4, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSBTAT000000292711ENSBTAE00000239030chr10:88254745-88254625121NPC2_BOVIN1-30303A:1-11
B:1-11
C:1-11		11
11
11
1.2ENSBTAT000000292712ENSBTAE00000239031chr10:88251066-88250959108NPC2_BOVIN30-66373A:11-47
B:11-47
C:11-47		37
37
37
1.3ENSBTAT000000292713ENSBTAE00000239032chr10:88249421-88249249173NPC2_BOVIN66-123583A:47-104
B:47-104
C:47-104		58
58
58
1.4ENSBTAT000000292714ENSBTAE00000239033chr10:88247010-88246163848NPC2_BOVIN124-151283A:105-130
B:105-130
C:105-130		26
26
26

(-) 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:130
 aligned with NPC2_BOVIN | P79345 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:130
                                    29        39        49        59        69        79        89        99       109       119       129       139       149
           NPC2_BOVIN    20 EPVKFKDCGSWVGVIKEVNVSPCPTQPCKLHRGQSYSVNVTFTSNTQSQSSKAVVHGIVMGIPVPFPIPESDGCKSGIRCPIEKDKTYNYVNKLPVKNEYPSIKVVVEWELTDDKNQRFFCWQIPIEVEA 149
               SCOP domains d2hkaa_ A: Epididymal secretory protein E1 (Niemann-Pick C2 protein)                                                               SCOP domains
               CATH domains 2hkaA00 A:1-130  [code=2.60.40.770, no name defined]                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.....eeeeeeeee......eeee...eeeeeeeeee.......eeeeeeee..eeee......hhhhh..........eeeeeeeee........eeeeeeeee.....eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1   -----------------------------------Exon 1.3  PDB: A:47-104 UniProt: 66-123                   Exon 1.4  PDB: A:105-130   Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.2  PDB: A:11-47 UniProt: 30-66----------------------------------------------------------------------------------- Transcript 1 (2)
                 2hka A   1 EPVKFKDCGSWVGVIKEVNVSPCPTQPCKLHRGQSYSVNVTFTSNTQSQSSKAVVHGIVMGIPVPFPIPESDGCKSGIRCPIEKDKTYNYVNKLPVKNEYPSIKVVVEWELTDDKNQRFFCWQIPIEVEA 130
                                    10        20        30        40        50        60        70        80        90       100       110       120       130


Chain B from PDB  Type:PROTEIN  Length:130
 aligned with NPC2_BOVIN | P79345 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:130
                                    29        39        49        59        69        79        89        99       109       119       129       139       149
           NPC2_BOVIN    20 EPVKFKDCGSWVGVIKEVNVSPCPTQPCKLHRGQSYSVNVTFTSNTQSQSSKAVVHGIVMGIPVPFPIPESDGCKSGIRCPIEKDKTYNYVNKLPVKNEYPSIKVVVEWELTDDKNQRFFCWQIPIEVEA 149
               SCOP domains d2hkab_ B: Epididymal secretory protein E1 (Niemann-Pick C2 protein)                                                               SCOP domains
               CATH domains 2hkaB00 B:1-130  [code=2.60.40.770, no name defined]                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.....eeeeeeeee......eeee...eeeeeeeeee.......eeeeeeee..eeee......hhhhh..........eeeeeeeee........eeeeeeeee.....eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1   -----------------------------------Exon 1.3  PDB: B:47-104 UniProt: 66-123                   Exon 1.4  PDB: B:105-130   Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.2  PDB: B:11-47 UniProt: 30-66----------------------------------------------------------------------------------- Transcript 1 (2)
                 2hka B   1 EPVKFKDCGSWVGVIKEVNVSPCPTQPCKLHRGQSYSVNVTFTSNTQSQSSKAVVHGIVMGIPVPFPIPESDGCKSGIRCPIEKDKTYNYVNKLPVKNEYPSIKVVVEWELTDDKNQRFFCWQIPIEVEA 130
                                    10        20        30        40        50        60        70        80        90       100       110       120       130


Chain C from PDB  Type:PROTEIN  Length:130
 aligned with NPC2_BOVIN | P79345 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:130
                                    29        39        49        59        69        79        89        99       109       119       129       139       149
           NPC2_BOVIN    20 EPVKFKDCGSWVGVIKEVNVSPCPTQPCKLHRGQSYSVNVTFTSNTQSQSSKAVVHGIVMGIPVPFPIPESDGCKSGIRCPIEKDKTYNYVNKLPVKNEYPSIKVVVEWELTDDKNQRFFCWQIPIEVEA 149
               SCOP domains d2hkac_ C: Epididymal secretory protein E1 (Niemann-Pick C2 protein)                                                               SCOP domains
               CATH domains 2hkaC00 C:1-130  [code=2.60.40.770, no name defined]                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.....eeeeeeeee......eeee...eeeeeeeeee.......eeeeeeee..eeee......hhhhh..........eeeeeeeee.......eeeeeeeeee.....eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1   -----------------------------------Exon 1.3  PDB: C:47-104 UniProt: 66-123                   Exon 1.4  PDB: C:105-130   Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.2  PDB: C:11-47 UniProt: 30-66----------------------------------------------------------------------------------- Transcript 1 (2)
                 2hka C   1 EPVKFKDCGSWVGVIKEVNVSPCPTQPCKLHRGQSYSVNVTFTSNTQSQSSKAVVHGIVMGIPVPFPIPESDGCKSGIRCPIEKDKTYNYVNKLPVKNEYPSIKVVVEWELTDDKNQRFFCWQIPIEVEA 130
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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, 3)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HKA)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (NPC2_BOVIN | P79345)
molecular function
    GO:0015485    cholesterol binding    Interacting selectively and non-covalently with 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:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    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:0033344    cholesterol efflux    The directed movement of cholesterol, cholest-5-en-3-beta-ol, out of a cell or organelle.
    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:0030301    cholesterol transport    The directed movement of cholesterol, cholest-5-en-3-beta-ol, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0032367    intracellular cholesterol transport    The directed movement of cholesterol, cholest-5-en-3-beta-ol, within cells.
    GO:0032366    intracellular sterol transport    The directed movement of sterols within cells.
    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:0009615    response to virus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a virus.
    GO:0008202    steroid metabolic process    The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
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: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:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.

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  2hka
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 Related Entries

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

UniProtKB/Swiss-Prot
        NPC2_BOVIN | P79345: 1nep

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