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- PDB-4ayw: STRUCTURE OF THE HUMAN MITOCHONDRIAL ABC TRANSPORTER, ABCB10 (PLA... -

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Basic information

Entry
Database: PDB / ID: 4ayw
TitleSTRUCTURE OF THE HUMAN MITOCHONDRIAL ABC TRANSPORTER, ABCB10 (PLATE FORM)
ComponentsATP-BINDING CASSETTE SUB-FAMILY B MEMBER 10
KeywordsMEMBRANE PROTEIN / MITOCHONDRIAL TRANSPORT
Function / homology
Function and homology information


positive regulation of heme biosynthetic process / Mitochondrial ABC transporters / mitochondrial unfolded protein response / positive regulation of hemoglobin biosynthetic process / erythrocyte development / heme biosynthetic process / mitochondrial transport / ABC-type transporter activity / positive regulation of erythrocyte differentiation / mitochondrial membrane ...positive regulation of heme biosynthetic process / Mitochondrial ABC transporters / mitochondrial unfolded protein response / positive regulation of hemoglobin biosynthetic process / erythrocyte development / heme biosynthetic process / mitochondrial transport / ABC-type transporter activity / positive regulation of erythrocyte differentiation / mitochondrial membrane / mitochondrial inner membrane / ATP hydrolysis activity / protein homodimerization activity / mitochondrion / ATP binding
Similarity search - Function
ABC transporter transmembrane region fold / ABC transporter type 1, transmembrane domain / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...ABC transporter transmembrane region fold / ABC transporter type 1, transmembrane domain / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / CHOLESTEROL HEMISUCCINATE / ATP-binding cassette sub-family B member 10, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.3 Å
AuthorsPike, A.C.W. / Shintre, C.A. / Li, Q. / Kim, J. / von Delft, F. / Barr, A.J. / Das, S. / Chaikuad, A. / Xia, X. / Quigley, A. ...Pike, A.C.W. / Shintre, C.A. / Li, Q. / Kim, J. / von Delft, F. / Barr, A.J. / Das, S. / Chaikuad, A. / Xia, X. / Quigley, A. / Dong, Y. / Dong, L. / Krojer, T. / Vollmar, M. / Muniz, J.R.C. / Bray, J.E. / Berridge, G. / Chalk, R. / Gileadi, O. / Burgess-Brown, N. / Shrestha, L. / Goubin, S. / Yang, J. / Mahajan, P. / Mukhopadhyay, S. / Bullock, A.N. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Edwards, A.M. / Carpenter, E.P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structures of Abcb10, a Human ATP-Binding Cassette Transporter in Apo- and Nucleotide-Bound States
Authors: Shintre, C.A. / Pike, A.C.W. / Li, Q. / Kim, J. / Barr, A.J. / von Delft, F. / Goub, S. / Shrestha, L. / Yang, J. / Berridge, G. / Ross, J. / Stansfeld, P.J. / Sansoa, M.S.P. / Edwards, M. / ...Authors: Shintre, C.A. / Pike, A.C.W. / Li, Q. / Kim, J. / Barr, A.J. / von Delft, F. / Goub, S. / Shrestha, L. / Yang, J. / Berridge, G. / Ross, J. / Stansfeld, P.J. / Sansoa, M.S.P. / Edwards, M. / Bountra, C. / Marsden, B.D. / von Delft, F. / Bullock, A.N. / Gileadi, O. / Burgess-Brown, N. / Carpenter, E.P.
History
DepositionJun 22, 2012Deposition site: PDBE / Processing site: PDBE
SupersessionJul 11, 2012ID: 4AA3
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references
Revision 1.2Jun 5, 2013Group: Database references / Structure summary
Revision 1.3Jun 12, 2013Group: Database references
Revision 1.4Aug 7, 2013Group: Database references
Revision 1.5Mar 25, 2015Group: Database references
Revision 1.6Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.7May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-BINDING CASSETTE SUB-FAMILY B MEMBER 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6484
Polymers67,1441
Non-polymers1,5043
Water0
1
A: ATP-BINDING CASSETTE SUB-FAMILY B MEMBER 10
hetero molecules

A: ATP-BINDING CASSETTE SUB-FAMILY B MEMBER 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,2968
Polymers134,2892
Non-polymers3,0076
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Buried area12200 Å2
ΔGint-101.8 kcal/mol
Surface area51620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.700, 101.700, 294.730
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein ATP-BINDING CASSETTE SUB-FAMILY B MEMBER 10 / ATP-BINDING CASSETTE TRANSPORTER 10 / ABC TRANSPORTER 10 PROTEIN / MITOCHONDRIAL ATP-BINDING ...ATP-BINDING CASSETTE TRANSPORTER 10 / ABC TRANSPORTER 10 PROTEIN / MITOCHONDRIAL ATP-BINDING CASSETTE 2 / M-ABC2


Mass: 67144.305 Da / Num. of mol.: 1 / Fragment: ABC TRANSPORTER, RESIDUES 1-5,126-738
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFB-LIC-BSE / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q9NRK6
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#4: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H50O4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.52 %
Description: DATA WERE HIGHLY ANISOTROPIC AND INTEGRATED WITH A SIGCUT 1.0 IN MOSFLM
Crystal growpH: 9.5
Details: 0.1 M SODIUM CHLORIDE, 5%(V/V)JEFFAMINE M-600, 0.1 M GLYCINE PH 9.5, 34%(V/V) PEG 400 CRYSTAL SOAKED BRIEFLY IN 10MM LUTETIUM CHLORIDE PRIOR TO DATA COLLECTION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.265
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.265 Å / Relative weight: 1
ReflectionResolution: 3.3→38.5 Å / Num. obs: 14186 / % possible obs: 98.4 % / Observed criterion σ(I): 1 / Redundancy: 9.1 % / Biso Wilson estimate: 86.82 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 11
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 3 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.2 / % possible all: 90.6

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXDSHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 3.3→37.99 Å / Cor.coef. Fo:Fc: 0.8859 / Cor.coef. Fo:Fc free: 0.8116 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.516
Details: 4AYT USED AS LSSR TARGET RESTRAINTS WITH A TARGET WEIGHT OF 0.1. THIS ENTRY HAS BEEN REREFINED WITH A MORE RECENT VERSION OF BUSTER V.2.11.2 AND REPLACES A PREVIOUS ENTRY 4AA3.
RfactorNum. reflection% reflectionSelection details
Rfree0.2861 585 4.14 %RANDOM
Rwork0.2506 ---
obs0.2522 14134 98.31 %-
Displacement parametersBiso mean: 109.09 Å2
Baniso -1Baniso -2Baniso -3
1--14.677 Å20 Å20 Å2
2---14.677 Å20 Å2
3---29.354 Å2
Refine analyzeLuzzati coordinate error obs: 0.985 Å
Refinement stepCycle: LAST / Resolution: 3.3→37.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4061 0 91 0 4152
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084233HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.945777HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1936SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes74HARMONIC2
X-RAY DIFFRACTIONt_gen_planes649HARMONIC5
X-RAY DIFFRACTIONt_it4233HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.96
X-RAY DIFFRACTIONt_other_torsion2.68
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion595SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4906SEMIHARMONIC4
LS refinement shellResolution: 3.3→3.56 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2844 108 4.08 %
Rwork0.2623 2538 -
all0.2632 2646 -
obs--98.31 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.08890.36940.1761.5297-1.44497.476-0.0009-0.3701-0.2619-0.2004-0.0884-0.15470.46230.62730.08930.0449-0.12430.0917-0.07540.0643-0.1706-25.565726.6117-34.6055
20.42070.12941.04090.5252-0.08091.3932-0.0711-0.183-0.05310.03-0.2150.00530.01450.1620.28610.1713-0.24340.06710.10460.0498-0.2202-14.846348.6026-33.7008
31.46351.5757-3.33922.1844-1.23672.5695-0.1155-0.2336-0.1970.19650.1069-0.1738-0.15050.31890.0087-0.1673-0.0858-0.08750.58220.3024-0.4024-15.526726.28983.442
48.7094-0.4912-0.34030.9485-1.83416.5293-0.2424-0.1699-0.34480.415-0.39890.1917-0.72180.8180.64130.2693-0.153-0.066-0.03630.1585-0.6161-34.373223.022115.2006
51.8410.3236-1.0656-0.242.78818.53860.0262-0.31390.22460.1411-0.14980.0995-0.25510.40620.12360.2416-0.0682-0.0430.30890.2594-0.4686-34.106226.094928.1226
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 154-276
2X-RAY DIFFRACTION2CHAIN A AND RESID 277 - 448
3X-RAY DIFFRACTION3CHAIN A AND RESID 449-513
4X-RAY DIFFRACTION4CHAIN A AND RESID 514-643
5X-RAY DIFFRACTION5CHAIN A AND RESID 644-717

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