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- PDB-3nha: Nucleotide Binding Domain of Human ABCB6 (ADP Mg bound structure) -

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Basic information

Entry
Database: PDB / ID: 3nha
TitleNucleotide Binding Domain of Human ABCB6 (ADP Mg bound structure)
ComponentsATP-binding cassette sub-family B member 6, mitochondrial
KeywordsTRANSPORT PROTEIN / ABC-transporter / ABCB6 / Nucleotide Binding Domain / heme biosynthesis
Function / homology
Function and homology information


cellular detoxification of cadmium ion / Defective ABCB6 causes MCOPCB7 / heme transmembrane transport / Mitochondrial ABC transporters / tetrapyrrole metabolic process / ABC-type heme transporter / ABC-type heme transporter activity / porphyrin-containing compound metabolic process / tetrapyrrole binding / heme transport ...cellular detoxification of cadmium ion / Defective ABCB6 causes MCOPCB7 / heme transmembrane transport / Mitochondrial ABC transporters / tetrapyrrole metabolic process / ABC-type heme transporter / ABC-type heme transporter activity / porphyrin-containing compound metabolic process / tetrapyrrole binding / heme transport / heme metabolic process / porphyrin-containing compound biosynthetic process / melanosome assembly / melanosome membrane / multivesicular body membrane / mitochondrial envelope / endolysosome membrane / vacuolar membrane / skin development / efflux transmembrane transporter activity / intracellular copper ion homeostasis / ABC-type transporter activity / ATP-binding cassette (ABC) transporter complex / brain development / transmembrane transport / early endosome membrane / intracellular iron ion homeostasis / mitochondrial outer membrane / endosome / lysosomal membrane / Golgi membrane / heme binding / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / mitochondrion / extracellular exosome / nucleoplasm / ATP binding / plasma membrane / cytosol
Similarity search - Function
Mitochondrial ABC-transporter, N-terminal five TM domain / Mitochondrial ABC-transporter N-terminal five TM region / 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 ...Mitochondrial ABC-transporter, N-terminal five TM domain / Mitochondrial ABC-transporter N-terminal five TM region / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BETA-MERCAPTOETHANOL / PHOSPHATE ION / ATP-binding cassette sub-family B member 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsHaffke, M. / Menzel, A. / Carius, Y. / Jahn, D. / Heinz, D.W.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Structures of the nucleotide-binding domain of the human ABCB6 transporter and its complexes with nucleotides.
Authors: Haffke, M. / Menzel, A. / Carius, Y. / Jahn, D. / Heinz, D.W.
History
DepositionJun 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Sep 6, 2023Group: 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_ref_seq_dif.details / _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 6, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1916
Polymers33,4881
Non-polymers7035
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.272, 70.708, 71.113
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ATP-binding cassette sub-family B member 6, mitochondrial / Mitochondrial ABC transporter 3 / Mt-ABC transporter 3 / Ubiquitously-expressed mammalian ABC half ...Mitochondrial ABC transporter 3 / Mt-ABC transporter 3 / Ubiquitously-expressed mammalian ABC half transporter / P-glycoprotein-related protein


Mass: 33487.766 Da / Num. of mol.: 1
Fragment: Nucleotide Binding Domain of the human ACB-transporter ABCB6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABCB6, MTABC3, PRP, UMAT / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner (DE3) / References: UniProt: Q9NP58

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Non-polymers , 5 types, 134 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.11 Å3/Da / Density % sol: 41.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES pH 6.5, 40% (v/v) PEG400, 3mM ADP, 3mM Magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.815 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Oct 15, 2009
RadiationMonochromator: Ge(111) triangular bent compressing 7 Fankuchen cut
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.815 Å / Relative weight: 1
ReflectionResolution: 2.1→44.1 Å / Num. all: 17131 / Num. obs: 17052 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 39.685 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 14.72
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.4 / Num. measured obs: 3480 / Num. unique all: 1149 / Num. unique obs: 1125 / % possible all: 97.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.31 Å19.69 Å
Translation2.31 Å19.69 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
AUTOMARdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NH6

3nh6


Resolution: 2.1→44.13 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.221 / WRfactor Rwork: 0.164 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.852 / SU B: 10.152 / SU ML: 0.128 / SU R Cruickshank DPI: 0.224 / SU Rfree: 0.202 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.252 853 5 %RANDOM
Rwork0.184 ---
obs0.187 17052 100 %-
all-17131 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 105.07 Å2 / Biso mean: 35.366 Å2 / Biso min: 15.03 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å20 Å20 Å2
2--1.08 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2111 0 41 129 2281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222189
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.9782964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6575280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.43323.7596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.71415371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4621519
X-RAY DIFFRACTIONr_chiral_restr0.1080.2343
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211626
X-RAY DIFFRACTIONr_mcbond_it0.8621.51377
X-RAY DIFFRACTIONr_mcangle_it1.47822207
X-RAY DIFFRACTIONr_scbond_it2.6733812
X-RAY DIFFRACTIONr_scangle_it4.0444.5755
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 61 -
Rwork0.241 1163 -
all-1224 -
obs-1220 100 %
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)
16.8556-0.31272.01883.62972.217312.94480.1444-0.0952-0.23920.0095-0.00260.09520.40420.0153-0.14180.0071-0.02390.00620.0691-0.07220.126329.309311.4644-35.5318
21.9445-0.55040.37743.4467-0.12612.24150.01330.15070.223-0.2446-0.0436-0.0914-0.20830.03390.03030.0504-0.02390.00070.07160.02420.042613.7489-2.8336-10.7125
37.02020.4003-0.25164.80441.20395.64630.06810.12140.3033-0.31020.1627-0.6655-0.27450.6578-0.23080.1459-0.03070.03950.1819-0.06490.157532.33077.48318.2549
42.0088-0.16460.27761.9689-0.45030.656-0.0419-0.2836-0.14870.17040.041-0.02330.03670.01250.00090.05390.00890.00710.12910.02610.054719.0472-15.05862.3264
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A550 - 573
2X-RAY DIFFRACTION2A574 - 672
3X-RAY DIFFRACTION3A673 - 742
4X-RAY DIFFRACTION4A743 - 828

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