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- PDB-4ayt: STRUCTURE OF THE HUMAN MITOCHONDRIAL ABC TRANSPORTER, ABCB10 -

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Basic information

Entry
Database: PDB / ID: 4ayt
TitleSTRUCTURE OF THE HUMAN MITOCHONDRIAL ABC TRANSPORTER, ABCB10
ComponentsATP-BINDING CASSETTE SUB-FAMILY B MEMBER 10 MITOCHONDRIAL
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 / heme biosynthetic process / erythrocyte development / 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 / heme biosynthetic process / erythrocyte development / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / 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. / 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. / 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
DepositionJun 22, 2012Deposition site: PDBE / Processing site: PDBE
SupersessionJul 11, 2012ID: 2YL4
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references / Structure summary
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_conn / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)69,8819
Polymers64,8171
Non-polymers5,0658
Water99155
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)139,76218
Polymers129,6332
Non-polymers10,12916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area14660 Å2
ΔGint-126.3 kcal/mol
Surface area53120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.110, 175.110, 49.550
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2002-

HOH

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Components

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Protein / Sugars , 2 types, 4 molecules A

#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


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
#5: 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

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Non-polymers , 5 types, 60 molecules

#2: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#6: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


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


Mass: 18.015 Da / Num. of mol.: 55 / 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: 3.39 Å3/Da / Density % sol: 63.71 % / Description: NONE
Crystal growpH: 9.5
Details: 0.1 M SODIUM CHLORIDE, 0.1 M GLYCINE PH 9.5, 37% (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: May 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.85→60 Å / Num. obs: 20523 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 70.87 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 7.7
Reflection shellResolution: 2.85→3 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AYW

4ayw


Resolution: 2.85→50.55 Å / Cor.coef. Fo:Fc: 0.8965 / Cor.coef. Fo:Fc free: 0.8599 / SU R Cruickshank DPI: 0.764 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.696 / SU Rfree Blow DPI: 0.322 / SU Rfree Cruickshank DPI: 0.331
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=4501. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=4501. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=1. THIS ENTRY HAS BEEN REREFINED WITH BUSTER 2.11.2, TO REPLACE 2YL4. RE-REFINEMENT OF A PROTEIN-ONLY MODEL GAVE WEAK DENSITY FOR SOME OF THE LIPID CHAINS MODELLED IN THE PREVIOUS (OBSOLETED) ENTRY (2YL4) AND THESE HAVE BEEN OMITTED FROM THE REVISED MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1064 5.19 %RANDOM
Rwork0.2006 ---
obs0.203 20519 99.69 %-
Displacement parametersBiso mean: 55.71 Å2
Baniso -1Baniso -2Baniso -3
1-3.297 Å20 Å20 Å2
2--3.297 Å20 Å2
3----6.594 Å2
Refine analyzeLuzzati coordinate error obs: 0.333 Å
Refinement stepCycle: LAST / Resolution: 2.85→50.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4227 0 211 55 4493
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094520HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.056109HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2151SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes85HARMONIC2
X-RAY DIFFRACTIONt_gen_planes669HARMONIC5
X-RAY DIFFRACTIONt_it4520HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.55
X-RAY DIFFRACTIONt_other_torsion3.26
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion605SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance4HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5393SEMIHARMONIC4
LS refinement shellResolution: 2.85→3 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.262 167 5.61 %
Rwork0.2146 2810 -
all0.2173 2977 -
obs--99.69 %

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