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(-) Description

Title :  STRUCTURE OF THE HUMAN MITOCHONDRIAL ABC TRANSPORTER, ABCB10 (ROD FORM B)
 
Authors :  A. C. W. Pike, C. A. Shintre, Q. Li, J. Kim, F. Von Delft, A. J. Barr, S. Das A. Chaikuad, X. Xia, A. Quigley, Y. Dong, L. Dong, T. Krojer, M. Vollmar J. R. C. Muniz, J. E. Bray, G. Berridge, R. Chalk, O. Gileadi, N. Burgess L. Shrestha, S. Goubin, J. Yang, P. Mahajan, S. Mukhopadhyay, A. N. Bul C. H. Arrowsmith, J. Weigelt, C. Bountra, A. M. Edwards, E. P. Carpente
Date :  22 Jun 12  (Deposition) - 11 Jul 12  (Release) - 25 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  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
    ChainsA
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF9
    Expression System CommonFALL ARMYWORM
    Expression System PlasmidPFB-LIC-BSE
    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

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 7)

Asymmetric Unit (5, 7)
No.NameCountTypeFull Name
1ACP1Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2CDL2Ligand/IonCARDIOLIPIN
3GLY1Mod. Amino AcidGLYCINE
4LMT2Ligand/IonDODECYL-BETA-D-MALTOSIDE
5MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (4, 12)
No.NameCountTypeFull Name
1ACP2Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2CDL4Ligand/IonCARDIOLIPIN
3GLY2Mod. Amino AcidGLYCINE
4LMT4Ligand/IonDODECYL-BETA-D-MALTOSIDE
5MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:534 , GLN A:575 , ASP A:658 , ACP A:900BINDING SITE FOR RESIDUE MG A 801
2AC2SOFTWARETYR A:501 , ILE A:509 , SER A:529 , GLY A:530 , SER A:531 , GLY A:532 , LYS A:533 , SER A:534 , THR A:535 , GLN A:575 , MG A:801BINDING SITE FOR RESIDUE ACP A 900
3AC3SOFTWAREARG A:170 , TYR A:234 , ARG A:242BINDING SITE FOR RESIDUE GLY A1717
4AC4SOFTWAREASP A:197 , TYR A:200 , THR A:201 , LEU A:218 , MET A:421 , GLY A:422 , THR A:427 , VAL A:428BINDING SITE FOR RESIDUE LMT A1720
5AC5SOFTWAREASN A:313 , THR A:316 , PHE A:317 , SER A:405 , LYS A:416 , LMT A:1724 , HOH A:2033BINDING SITE FOR RESIDUE CDL A1721
6AC6SOFTWARESER A:405 , ILE A:409 , SER A:412 , TYR A:415 , LYS A:416 , LEU A:420 , SER A:423 , HIS A:425 , CDL A:1721 , HOH A:2033BINDING SITE FOR RESIDUE LMT A1724
7AC7SOFTWAREILE A:184 , ASN A:229 , ASN A:407BINDING SITE FOR RESIDUE CDL A1726

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AYX)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4AYX)

 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 4AYX)

(-) 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:572
 aligned with ABCBA_HUMAN | Q9NRK6 from UniProtKB/Swiss-Prot  Length:738

    Alignment length:573
                                   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       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723   
         ABCBA_HUMAN    154 LPEARKLLGLAYPERRRLAAAVGFLTMSSVISMSAPFFLGKIIDVIYTNPTVDYSDNLTRLCLGLSAVFLCGAAANAIRVYLMQTSGQRIVNRLRTSLFSSILRQEVAFFDKTRTGELINRLSSDTALLGRSVTENLSDGLRAGAQASVGISMMFFVSPNLATFVLSVVPPVSIIAVIYGRYLRKLTKVTQDSLAQATQLAEERIGNVRTVRAFGKEMTEIEKYASKVDHVMQLARKEAFARAGFFGATGLSGNLIVLSVLYKGGLLMGSAHMTVGELSSFLMYAFWVGISIGGLSSFYSELMKGLGAGGRLWELLEREPKLPFNEGVILNEKSFQGALEFKNVHFAYPARPEVPIFQDFSLSIPSGSVTALVGPSGSGKSTVLSLLLRLYDPASGTISLDGHDIRQLNPVWLRSKIGTVSQEPILFSCSIAENIAYGADDPSSVTAEEIQRVAEVANAVAFIRNFPQGFNTVVGEKGVLLSGGQKQRIAIARALLKNPKILLLDEATSALDAENEYLVQEALDRLMDGRTVLVIAHRLSTIKNANMVAVLDQGKITEYGKHEELLSKPNGIY  726
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....................eeeeeeeee.......eeeeeeeeee....eeeee.......hhhhhhhh......eeeeee..ee....hhhhhhhheeee.........hhhhhhhh........hhhhhhhhhhhh.hhhhhhhh.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
                4ayx A  154 LPEARKLLGLAYPERRRLAAAVGFLTMSSVISMSAPFFLGKIIDVIYTNPTVDYSDNLTRLCLGLSAVFLCGAAANAIRVYLMQTSGQRIVNRLRTSLFSSILRQEVAFFDKTRTGELINRLSSDTALLGRSVTENLSDGLRAGAQASVGISMMFFVSPNLATFVLSVVPPVSIIAVIYGRYLRKLTKVTQDSLAQATQLAEERIGNVRTVRAFGKEMTEIEKYASKVDHVMQLARKEAFARAGFFGATGLSGNLIVLSVLYKGGLLMGSAHMTVGELSSFLMYAFWVGISIGGLSSFYSELMKGLGAGGRLWELLEREPKLPFNEGVILNEKSFQGALEFKNVHFAYPARPEVPIFQDFSLSIPSGSVTALVGPSGSGKSTVLSLLLRLYDPASGTISLDGHDIRQLNPVWLRSKIGTVSQEPILFSCSIAENIAYGADDPSSVTAEEIQRVAEVANAVAFIRNFPQGFNTVVGEKGVLLSGGQKQRIAIARALLKNPKILLLDEATSALDAENEYLVQEALDRLMDGRTVLVIAHRLSTIKNANMVAVLDQGKITEYGKHEELLSKPNG-G 1717
                                   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       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723| |
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    724 |
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     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 4AYX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 | Q9NRK63zdq 4ayt 4ayw

(-) Related Entries Specified in the PDB File

4ayt STRUCTURE OF THE HUMAN MITOCHONDRIAL ABC TRANSPORTER, ABCB10
4ayw STRUCTURE OF THE HUMAN MITOCHONDRIAL ABC TRANSPORTER, ABCB10 (PLATE FORM)