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- PDB-5och: The crystal structure of human ABCB8 in an outward-facing state -

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Basic information

Entry
Database: PDB / ID: 5och
TitleThe crystal structure of human ABCB8 in an outward-facing state
Components(ATP-binding cassette sub-family B member 8, ...) x 5
KeywordsHYDROLASE / Membrane protein / ATP binding / ATP binding cassette / half transporter / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


mitochondrial ATP-gated potassium channel complex / mitochondrial potassium ion transmembrane transport / Mitochondrial ABC transporters / cell volume homeostasis / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / potassium ion transmembrane transport / ATP-binding cassette (ABC) transporter complex / mitochondrial membrane / transmembrane transport ...mitochondrial ATP-gated potassium channel complex / mitochondrial potassium ion transmembrane transport / Mitochondrial ABC transporters / cell volume homeostasis / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / potassium ion transmembrane transport / ATP-binding cassette (ABC) transporter complex / mitochondrial membrane / transmembrane transport / mitochondrial inner membrane / nucleolus / ATP hydrolysis activity / mitochondrion / nucleoplasm / ATP binding / membrane
Similarity search - Function
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. ...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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / CHOLESTEROL HEMISUCCINATE / Mitochondrial potassium channel ATP-binding subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsFaust, B. / Pike, A.C.W. / Shintre, C.A. / Quiqley, A.M. / Chu, A. / Barr, A. / Shrestha, L. / Mukhopadhyay, S. / Borkowska, O. / Chalk, R. ...Faust, B. / Pike, A.C.W. / Shintre, C.A. / Quiqley, A.M. / Chu, A. / Barr, A. / Shrestha, L. / Mukhopadhyay, S. / Borkowska, O. / Chalk, R. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Carpenter, E.P. / Structural Genomics Consortium (SGC)
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: To Be Published
Title: The crystal structure of human ABCB8 in an outward-facing state
Authors: Faust, B. / Pike, A.C.W. / Shintre, C.A. / Quiqley, A.M. / Chu, A. / Barr, A. / Shrestha, L. / Mukhopadhyay, S. / Borkowska, O. / Chalk, R. / Burgess-Brown, N.A. / Arrowsmith, C.H. / ...Authors: Faust, B. / Pike, A.C.W. / Shintre, C.A. / Quiqley, A.M. / Chu, A. / Barr, A. / Shrestha, L. / Mukhopadhyay, S. / Borkowska, O. / Chalk, R. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Carpenter, E.P.
History
DepositionJun 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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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 8, mitochondrial
B: ATP-binding cassette sub-family B member 8, mitochondrial
C: ATP-binding cassette sub-family B member 8, mitochondrial
D: ATP-binding cassette sub-family B member 8, mitochondrial
E: ATP-binding cassette sub-family B member 8, mitochondrial
F: ATP-binding cassette sub-family B member 8, mitochondrial
G: ATP-binding cassette sub-family B member 8, mitochondrial
H: ATP-binding cassette sub-family B member 8, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)539,51731
Polymers532,4988
Non-polymers7,01923
Water00
1
A: ATP-binding cassette sub-family B member 8, mitochondrial
B: ATP-binding cassette sub-family B member 8, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,0158
Polymers133,1392
Non-polymers1,8766
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13300 Å2
ΔGint-117 kcal/mol
Surface area48040 Å2
MethodPISA
2
C: ATP-binding cassette sub-family B member 8, mitochondrial
D: ATP-binding cassette sub-family B member 8, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,4717
Polymers133,0822
Non-polymers1,3905
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11770 Å2
ΔGint-110 kcal/mol
Surface area49130 Å2
MethodPISA
3
E: ATP-binding cassette sub-family B member 8, mitochondrial
F: ATP-binding cassette sub-family B member 8, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,0728
Polymers133,1962
Non-polymers1,8766
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12910 Å2
ΔGint-119 kcal/mol
Surface area48580 Å2
MethodPISA
4
G: ATP-binding cassette sub-family B member 8, mitochondrial
H: ATP-binding cassette sub-family B member 8, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,9588
Polymers133,0822
Non-polymers1,8766
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11770 Å2
ΔGint-110 kcal/mol
Surface area48880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.080, 98.500, 214.870
Angle α, β, γ (deg.)90.00, 90.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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ATP-binding cassette sub-family B member 8, ... , 5 types, 8 molecules ACDBEFGH

#1: Protein ATP-binding cassette sub-family B member 8, mitochondrial / Mitochondrial ATP-binding cassette 1 / M-ABC1


Mass: 66540.805 Da / Num. of mol.: 3 / Fragment: UNP residues 111-714
Source method: isolated from a genetically manipulated source
Details: Protein was alkylated with iodoacetamide prior to crystallisation
Source: (gene. exp.) Homo sapiens (human) / Gene: ABCB8, MABC1 / Plasmid: pFB-CT10HF-LIC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NUT2
#2: Protein ATP-binding cassette sub-family B member 8, mitochondrial / Mitochondrial ATP-binding cassette 1 / M-ABC1


Mass: 66597.859 Da / Num. of mol.: 1 / Fragment: UNP residues 111-714
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABCB8, MABC1 / Plasmid: pFB-CT10HF-LIC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NUT2
#3: Protein ATP-binding cassette sub-family B member 8, mitochondrial / Mitochondrial ATP-binding cassette 1 / M-ABC1


Mass: 66597.859 Da / Num. of mol.: 1 / Fragment: UNP residues 111-714
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABCB8, MABC1 / Plasmid: pFB-CT10HF-LIC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NUT2
#4: Protein ATP-binding cassette sub-family B member 8, mitochondrial / Mitochondrial ATP-binding cassette 1 / M-ABC1


Mass: 66597.859 Da / Num. of mol.: 2 / Fragment: UNP residues 111-714
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABCB8, MABC1 / Plasmid: pFB-CT10HF-LIC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NUT2
#5: Protein ATP-binding cassette sub-family B member 8, mitochondrial / Mitochondrial ATP-binding cassette 1 / M-ABC1


Mass: 66483.750 Da / Num. of mol.: 1 / Fragment: UNP residues 111-714
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABCB8, MABC1 / Plasmid: pFB-CT10HF-LIC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NUT2

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Non-polymers , 3 types, 23 molecules

#6: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#8: Chemical
ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 7 / 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: 3.6 Å3/Da / Density % sol: 65.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES pH 7.5 -- 18% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.4→72.61 Å / Num. obs: 104497 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 122.428 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.22 / Rpim(I) all: 0.09 / Net I/σ(I): 7
Reflection shellResolution: 3.4→3.46 Å / Redundancy: 6.8 % / Rmerge(I) obs: 7.3 / Mean I/σ(I) obs: 0.3 / Num. unique obs: 5020 / CC1/2: 0.078 / Rpim(I) all: 2.984 / % possible all: 98

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZDQ

3zdq


Resolution: 3.4→72.61 Å / Cor.coef. Fo:Fc: 0.8701 / Cor.coef. Fo:Fc free: 0.8638 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.667
Details: DATA WERE ANISOTROPICALLY TRUNCATED TO 3.4A PRIOR TO REFINEMENT USING STARANISO SERVER. ANISOTROPIC CUTOFFS WERE 5.14A, 5.44A and 3.4A RESPECTIVELY. DATA COMPLETENESS DROPS OFF MARKEDLY ...Details: DATA WERE ANISOTROPICALLY TRUNCATED TO 3.4A PRIOR TO REFINEMENT USING STARANISO SERVER. ANISOTROPIC CUTOFFS WERE 5.14A, 5.44A and 3.4A RESPECTIVELY. DATA COMPLETENESS DROPS OFF MARKEDLY ABOVE 4A RESOLUTION BUT THIS APPROACH RESULTED IN IMPROVED MAP QUALITY. AFTER TRUNCATION CC1/2 IN HIGH RESOLUTION SHELL WAS 0.5485. A SINGLE TLS GROUP PER PROTEIN CHAIN WAS USED. MAPS WERE SHARPENED IN COOT USING A -100A**2 FOR MODEL BUILDING. BOTH TRUNCATED AND UNTRUNCATED SF DATA ARE PRESENT IN ASSOCIATED SF FILE
RfactorNum. reflection% reflectionSelection details
Rfree0.251 3147 4.85 %RANDOM
Rwork0.231 ---
obs0.232 64839 61.9 %-
Displacement parametersBiso mean: 137.29 Å2
Baniso -1Baniso -2Baniso -3
1-2.699 Å20 Å21.6687 Å2
2---2.3786 Å20 Å2
3----0.3204 Å2
Refine analyzeLuzzati coordinate error obs: 0.604 Å
Refinement stepCycle: 1 / Resolution: 3.4→72.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30741 0 427 0 31168
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00831763HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9343389HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d14148SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes516HARMONIC2
X-RAY DIFFRACTIONt_gen_planes5106HARMONIC5
X-RAY DIFFRACTIONt_it31763HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.62
X-RAY DIFFRACTIONt_other_torsion2.51
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4479SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance16HARMONIC1
X-RAY DIFFRACTIONt_utility_angle8HARMONIC1
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact34689SEMIHARMONIC4
LS refinement shellResolution: 3.4→3.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2662 49 4.79 %
Rwork0.2512 975 -
all0.252 1024 -
obs--13.27 %
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)
11.69290.2033-0.20190.8117-1.30416.00060.264-0.31750.14190.2395-0.0761-0.2351-0.4290.8467-0.1879-0.2138-0.0547-0.1368-0.2227-0.0908-0.309202.539715.4878458.8279
22.41240.10350.90750.4647-0.04652.88640.1397-0.4402-0.09770.2256-0.0059-0.053-0.12390.069-0.1338-0.2316-0.0297-0.0692-0.45110.0334-0.2746183.67734.8783461.5504
31.08780.10960.7020.8864-0.92396.30330.06540.07930.296-0.04940.0231-0.5201-0.76821.0221-0.0885-0.1682-0.23970.18120.5279-0.21790.4528247.417357.8419430.7735
42.102-0.31261.99160.7117-0.24143.65670.2494-0.12870.24940.03780.0057-0.4069-0.10140.348-0.255-0.2806-0.10530.0768-0.0589-0.1360.034227.556749.1382434.9953
52.18090.1445-0.93980.9583-1.3566.44390.0752-0.75340.1248-0.0780.0326-0.28441.0341.0837-0.10780.31220.0033-0.05220.059-0.105-0.264156.888345.6614504.2873
62.82980.3532-2.97020.492-0.90524.58060.1985-0.52220.39320.06060.10120.10950.02210.2841-0.29970.0534-0.2524-0.003-0.3461-0.11-0.2424136.871453.8691502.8126
72.3580.103-2.17550.55780.36635.57060.33650.22530.04320.03040.02490.0627-0.1005-0.1528-0.36130.08030.11120.1044-0.35080.06810.0483260.286149.1933539.821
81.6047-0.0705-0.31331.20170.89455.26790.20250.3575-0.23180.0525-0.22470.42760.7687-0.89750.02220.0547-0.02450.12110.2752-0.01610.0818241.078738.659540.0123
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|132 - 718}
2X-RAY DIFFRACTION2{B|132 - 718}
3X-RAY DIFFRACTION3{C|132 - 718}
4X-RAY DIFFRACTION4{D|132 - 713}
5X-RAY DIFFRACTION5{E|132 - 716}
6X-RAY DIFFRACTION6{F|132 - 712}
7X-RAY DIFFRACTION7{G|132 - 717}
8X-RAY DIFFRACTION8{H|132 - 713}

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