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(-) Description

Title :  STRUCTURE OF THE HUMAN MITOCHONDRIAL ABC TRANSPORTER, ABCB10 (NUCLEOTIDE-FREE FORM)
 
Authors :  A. C. W. Pike, C. A. Shintre, T. Krojer, F. Von Delft, M. Vollmar, S. Mukh N. Burgess-Brown, C. H. Arrowsmith, C. Bountra, A. M. Edwards, E. P. Ca
Date :  30 Nov 12  (Deposition) - 23 Jan 13  (Release) - 25 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hydrolase, Membrane Protein, Mitochondrial Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. A. Shintre, A. C. W. Pike, Q. Li, J. Kim, A. J. Barr, S. Goubin, L. Shrestha, J. Yang, G. Berridge, J. Ross, P. J. Stansfeld, M. S. P. Sansom, A. M. Edwards, C. Bountra, B. D. Marsden, F. Von Delft, A. N. Bullock, O. Gileadi, N. A. Burgess-Brown, E. P. Carpenter
Structures Of Abcb10, A Human Atp-Binding Cassette Transporter In Apo- And Nucleotide-Bound States
Proc. Natl. Acad. Sci. Usa V. 110 9710 2013
PubMed-ID: 23716676  |  Reference-DOI: 10.1073/PNAS.1217042110

(-) Compounds

Molecule 1 - ATP-BINDING CASSETTE SUB-FAMILY B MEMBER 10, MITOCHONDRIAL
    ChainsA
    EC Number3.6.3.43
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF9
    Expression System CommonFALL ARMYWORM
    Expression System PlasmidPFB-CT10HF-LIC
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    FragmentABC TRANSPORTER, RESIDUES 152-738
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymATP-BINDING CASSETTE TRANSPORTER 10, ABC TRANSPORTER 10 PROTEIN, MITOCHONDRIAL ATP-BINDING CASSETTE 2, M-ABC2, ATP-BINDING CASSETTE SUB-FAMILY B MEMBER 10

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1CDL2Ligand/IonCARDIOLIPIN
2GLY1Mod. Amino AcidGLYCINE
3LMT3Ligand/IonDODECYL-BETA-D-MALTOSIDE
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1CDL4Ligand/IonCARDIOLIPIN
2GLY2Mod. Amino AcidGLYCINE
3LMT6Ligand/IonDODECYL-BETA-D-MALTOSIDE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:170 , TYR A:234 , ARG A:242BINDING SITE FOR RESIDUE GLY A1717
2AC2SOFTWAREASP A:197 , TYR A:200 , THR A:201 , PRO A:203 , GLY A:418 , MET A:421 , THR A:427 , VAL A:428 , ASN A:484BINDING SITE FOR RESIDUE LMT A1720
3AC3SOFTWAREPHE A:308 , PRO A:312 , ASN A:313 , THR A:316 , PHE A:317 , PRO A:324 , SER A:405 , LYS A:416 , LMT A:1724BINDING SITE FOR RESIDUE CDL A1721
4AC4SOFTWAREVAL A:322 , ALA A:438 , SER A:449BINDING SITE FOR RESIDUE LMT A1723
5AC5SOFTWARESER A:405 , SER A:412 , TYR A:415 , LYS A:416 , LEU A:420 , SER A:423 , HIS A:425 , CDL A:1721 , HOH A:2017BINDING SITE FOR RESIDUE LMT A1724
6AC6SOFTWAREMET A:180 , SER A:181 , ILE A:184 , ASN A:229BINDING SITE FOR RESIDUE CDL A1728

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048133R242GABCBA_HUMANPolymorphism17584642AR242G
2UniProtVAR_035735R471TABCBA_HUMANUnclassified  ---AR471T
3UniProtVAR_031435D545NABCBA_HUMANPolymorphism35698797AD545N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048133R242GABCBA_HUMANPolymorphism17584642AR242G
2UniProtVAR_035735R471TABCBA_HUMANUnclassified  ---AR471T
3UniProtVAR_031435D545NABCBA_HUMANPolymorphism35698797AD545N

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ABC_TM1FPS50929 ABC transporter integral membrane type-1 fused domain profile.ABCBA_HUMAN172-457  1A:172-457
2ABC_TRANSPORTER_1PS00211 ABC transporters family signature.ABCBA_HUMAN634-648  1A:634-648
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ABC_TM1FPS50929 ABC transporter integral membrane type-1 fused domain profile.ABCBA_HUMAN172-457  2A:172-457
2ABC_TRANSPORTER_1PS00211 ABC transporters family signature.ABCBA_HUMAN634-648  2A:634-648

(-) Exons   (0, 0)

(no "Exon" information available for 3ZDQ)

(-) 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:571
 aligned with ABCBA_HUMAN | Q9NRK6 from UniProtKB/Swiss-Prot  Length:738

    Alignment length:572
                                   162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722  
         ABCBA_HUMAN    153 GLPEARKLLGLAYPERRRLAAAVGFLTMSSVISMSAPFFLGKIIDVIYTNPTVDYSDNLTRLCLGLSAVFLCGAAANAIRVYLMQTSGQRIVNRLRTSLFSSILRQEVAFFDKTRTGELINRLSSDTALLGRSVTENLSDGLRAGAQASVGISMMFFVSPNLATFVLSVVPPVSIIAVIYGRYLRKLTKVTQDSLAQATQLAEERIGNVRTVRAFGKEMTEIEKYASKVDHVMQLARKEAFARAGFFGATGLSGNLIVLSVLYKGGLLMGSAHMTVGELSSFLMYAFWVGISIGGLSSFYSELMKGLGAGGRLWELLEREPKLPFNEGVILNEKSFQGALEFKNVHFAYPARPEVPIFQDFSLSIPSGSVTALVGPSGSGKSTVLSLLLRLYDPASGTISLDGHDIRQLNPVWLRSKIGTVSQEPILFSCSIAENIAYGADDPSSVTAEEIQRVAEVANAVAFIRNFPQGFNTVVGEKGVLLSGGQKQRIAIARALLKNPKILLLDEATSALDAENEYLVQEALDRLMDGRTVLVIAHRLSTIKNANMVAVLDQGKITEYGKHEELLSKPNG  724
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....................eeeeeeee..........eeeeeeee....eeeee..hhhhhhhhhhhhh......eeeeee..ee....hhhhhhhheeee.........hhhhhhhh........hhhhhhhhhhhh.hhhhhhh..hhhhh.........hhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhh.eeeee....eeeeehhhhhhh..-. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------G------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T-------------------------------------------------------------------------N----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------ABC_TM1F  PDB: A:172-457 UniProt: 172-457                                                                                                                                                                                                                                                     --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ABC_TRANSPORTER---------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3zdq A  153 GLPEARKLLGLAYPERRRLAAAVGFLTMSSVISMSAPFFLGKIIDVIYTNPTVDYSDNLTRLCLGLSAVFLCGAAANAIRVYLMQTSGQRIVNRLRTSLFSSILRQEVAFFDKTRTGELINRLSSDTALLGRSVTENLSDGLRAGAQASVGISMMFFVSPNLATFVLSVVPPVSIIAVIYGRYLRKLTKVTQDSLAQATQLAEERIGNVRTVRAFGKEMTEIEKYASKVDHVMQLARKEAFARAGFFGATGLSGNLIVLSVLYKGGLLMGSAHMTVGELSSFLMYAFWVGISIGGLSSFYSELMKGLGAGGRLWELLEREPKLPFNEGVILNEKSFQGALEFKNVHFAYPARPEVPIFQDFSLSIPSGSVTALVGPSGSGKSTVLSLLLRLYDPASGTISLDGHDIRQLNPVWLRSKIGTVSQEPILFSCSIAENIAYGADDPSSVTAEEIQRVAEVANAVAFIRNFPQGFNTVVGEKGVLLSGGQKQRIAIARALLKNPKILLLDEATSALDAENEYLVQEALDRLMDGRTVLVIAHRLSTIKNANMVAVLDQGKITEYGKHEELLSKP-G 1717
                                   162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722 |
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   722 |
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    1717

   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 3ZDQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A   (ABCBA_HUMAN | Q9NRK6)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0042626    ATPase activity, coupled to transmembrane movement of substances    Catalysis of the reaction: ATP + H2O = ADP + phosphate, to directly drive the active transport of a substance across a membrane.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
    GO:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0032592    integral component of mitochondrial membrane    The component of the mitochondrial membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ABCBA_HUMAN | Q9NRK64ayt 4ayw 4ayx

(-) Related Entries Specified in the PDB File

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