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- PDB-3zdq: STRUCTURE OF THE HUMAN MITOCHONDRIAL ABC TRANSPORTER, ABCB10 (NUC... -

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Basic information

Entry
Database: PDB / ID: 3zdq
TitleSTRUCTURE OF THE HUMAN MITOCHONDRIAL ABC TRANSPORTER, ABCB10 (NUCLEOTIDE-FREE FORM)
ComponentsATP-BINDING CASSETTE SUB-FAMILY B MEMBER 10, MITOCHONDRIAL
KeywordsHYDROLASE / MEMBRANE PROTEIN / MITOCHONDRIAL TRANSPORT
Function / homology
Function and homology information


export from the mitochondrion / positive regulation of heme biosynthetic process / Mitochondrial ABC transporters / mitochondrial unfolded protein response / positive regulation of hemoglobin biosynthetic process / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / heme biosynthetic process / mitochondrial transport / ABC-type transporter activity / erythrocyte development ...export from the mitochondrion / positive regulation of heme biosynthetic process / Mitochondrial ABC transporters / mitochondrial unfolded protein response / positive regulation of hemoglobin biosynthetic process / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / heme biosynthetic process / mitochondrial transport / ABC-type transporter activity / erythrocyte development / positive regulation of erythrocyte differentiation / mitochondrial membrane / mitochondrial inner membrane / protein homodimerization activity / ATP hydrolysis activity / mitochondrion / ATP binding / metal ion 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CARDIOLIPIN / GLYCINE / ATP-binding cassette sub-family B member 10, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsPike, A.C.W. / Shintre, C.A. / Krojer, T. / von Delft, F. / Vollmar, M. / Mukhopadhyay, S. / Burgess-Brown, N. / Arrowsmith, C.H. / 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. / Goubin, S. / Shrestha, L. / Yang, J. / Berridge, G. / Ross, J. / Stansfeld, P.J. / Sansom, M.S.P. / Edwards, A.M. / Bountra, C. ...Authors: Shintre, C.A. / Pike, A.C.W. / Li, Q. / Kim, J. / Barr, A.J. / Goubin, S. / Shrestha, L. / Yang, J. / Berridge, G. / Ross, J. / Stansfeld, P.J. / Sansom, M.S.P. / Edwards, A.M. / Bountra, C. / Marsden, B.D. / von Delft, F. / Bullock, A.N. / Gileadi, O. / Burgess-Brown, N.A. / Carpenter, E.P.
History
DepositionNov 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Jun 12, 2013Group: Database references
Revision 1.3Jun 26, 2013Group: Database references
Revision 1.4Mar 25, 2015Group: Database references
Revision 1.5Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.6Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)69,3527
Polymers64,8171
Non-polymers4,5356
Water54030
1
A: ATP-BINDING CASSETTE SUB-FAMILY B MEMBER 10, MITOCHONDRIAL
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)138,70314
Polymers129,6332
Non-polymers9,07012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area17580 Å2
ΔGint-103.5 kcal/mol
Surface area54130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.790, 177.790, 50.060
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein ATP-BINDING CASSETTE SUB-FAMILY B MEMBER 10, MITOCHONDRIAL / 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 / ATP-BINDING CASSETTE SUB-FAMILY B MEMBER 10


Mass: 64816.684 Da / Num. of mol.: 1 / Fragment: ABC TRANSPORTER, RESIDUES 152-738
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFB-CT10HF-LIC / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q9NRK6, EC: 3.6.3.43
#2: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#4: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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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: 3.53 Å3/Da / Density % sol: 65.22 % / Description: NONE
Crystal growpH: 9.25
Details: 0.1M SODIUM CHLORIDE, 0.1M GLYCINE PH 9.25, 30%(V/V) PEG 300

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.85→38.49 Å / Num. obs: 21419 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 84.5 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.3
Reflection shellResolution: 2.85→2.92 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AYT

4ayt


Resolution: 2.85→30.52 Å / Cor.coef. Fo:Fc: 0.9144 / Cor.coef. Fo:Fc free: 0.8869 / SU R Cruickshank DPI: 0.645 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.584 / SU Rfree Blow DPI: 0.307 / SU Rfree Cruickshank DPI: 0.318
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2444 1101 5.15 %RANDOM
Rwork0.2021 ---
obs0.2042 21397 99.97 %-
Displacement parametersBiso mean: 75 Å2
Baniso -1Baniso -2Baniso -3
1-7.47 Å20 Å20 Å2
2--7.47 Å20 Å2
3----14.94 Å2
Refine analyzeLuzzati coordinate error obs: 0.393 Å
Refinement stepCycle: LAST / Resolution: 2.85→30.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4239 0 186 30 4455
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014506HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.066084HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2145SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes81HARMONIC2
X-RAY DIFFRACTIONt_gen_planes659HARMONIC5
X-RAY DIFFRACTIONt_it4506HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.47
X-RAY DIFFRACTIONt_other_torsion3.23
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion608SEMIHARMONIC5
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_contact5197SEMIHARMONIC4
LS refinement shellResolution: 2.85→2.99 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.244 157 5.56 %
Rwork0.2178 2667 -
all0.2194 2824 -
obs--99.97 %
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)
10.9666-0.9080.10113.41440.61370.18920.14830.10890.0158-0.1690.1120.19330.1074-0.1986-0.2603-0.03720.0750.096-0.16790.06890.0779-64.066876.86577.9985
2-0.3360.4394-0.01171.3898-0.870900.15910.1099-0.0674-0.1710.00280.27830.0405-0.1442-0.16180.10560.0953-0.0057-0.18430.05290.0356-48.788360.1393-0.5699
31.8459-2.87271.3214.4136-1.17820.6760.26190.15730.043-0.407-0.1715-0.1186-0.2505-0.1105-0.0904-0.07740.20680.0246-0.04010.02-0.037-15.394262.28970.3814
40.5167-0.3719-0.03373.1973-0.633800.03170.0814-0.01170.0395-0.00140.0385-0.0716-0.052-0.03030.01750.1076-0.0087-0.1301-0.0001-0.1516-42.179450.4873-3.0227
52.2343-0.4636-0.45872.95571.08986.395-0.0257-0.3165-0.2640.33950.1136-0.2245-0.01320.6313-0.0878-0.2506-0.0002-0.0821-0.25820.0717-0.0204-31.571216.66213.415
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESSEQ 153 - 232
2X-RAY DIFFRACTION2CHAIN A AND RESSEQ 233 - 331
3X-RAY DIFFRACTION3CHAIN A AND RESSEQ 332 - 397
4X-RAY DIFFRACTION4CHAIN A AND RESSEQ 398 - 528
5X-RAY DIFFRACTION5CHAIN A AND RESSEQ 529 - 722

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