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- PDB-3wme: Crystal structure of an inward-facing eukaryotic ABC multidrug tr... -

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Basic information

Entry
Database: PDB / ID: 3wme
TitleCrystal structure of an inward-facing eukaryotic ABC multidrug transporter
ComponentsATP-binding cassette, sub-family B, member 1
KeywordsTRANSPORT PROTEIN / Rec fold / Multi drug transporter
Function / homology
Function and homology information


ABC-type transporter activity / chloroplast / ATP hydrolysis activity / ATP binding / membrane / 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
Probable ATP-dependent transporter ycf16
Similarity search - Component
Biological speciesCyanidioschyzon merolae (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.751 Å
AuthorsKodan, A. / Yamaguchi, T. / Nakatsu, T. / Kato, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural basis for gating mechanisms of a eukaryotic P-glycoprotein homolog.
Authors: Kodan, A. / Yamaguchi, T. / Nakatsu, T. / Sakiyama, K. / Hipolito, C.J. / Fujioka, A. / Hirokane, R. / Ikeguchi, K. / Watanabe, B. / Hiratake, J. / Kimura, Y. / Suga, H. / Ueda, K. / Kato, H.
History
DepositionNov 18, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references / Source and taxonomy
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6162
Polymers66,1341
Non-polymers4831
Water36020
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ATP-binding cassette, sub-family B, member 1
hetero molecules

A: ATP-binding cassette, sub-family B, member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,2324
Polymers132,2672
Non-polymers9652
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area11260 Å2
ΔGint-97 kcal/mol
Surface area50790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.312, 180.312, 152.332
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein ATP-binding cassette, sub-family B, member 1


Mass: 66133.680 Da / Num. of mol.: 1 / Fragment: TMD and NBD domain, UNP RESIDUES 93-696
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanidioschyzon merolae (eukaryote) / Strain: 10D / Gene: CMD148C, CYME_CMD148C / Plasmid: pPICZ-A / Production host: Komagataella pastoris (fungus) / Strain (production host): SMD1163 / References: UniProt: M1VAN7
#2: Sugar ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.6 Å3/Da / Density % sol: 65.86 % / Mosaicity: 0.441 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 15% (w/v) PEG 2000 MME, 100mM magnesium nitrate, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9929, 1.0000, 1.0053, 1.0060, 1.0091
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 3, 2010
RadiationMonochromator: double-crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.99291
211
31.00531
41.0061
51.00911
ReflectionRedundancy: 11.3 % / Number: 204173 / Rmerge(I) obs: 0.071 / Χ2: 2.54 / D res high: 3.1 Å / D res low: 50 Å / Num. obs: 18055 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
8.45096.210.0425.72210.5
6.678.410010.0545.01711.1
5.836.6710010.0775.53510.9
5.35.8310010.0734.4210.8
4.925.310010.0693.77211.2
4.634.9210010.0592.92711.3
4.44.6310010.0562.42111.4
4.214.410010.062.21211.4
4.044.2110010.0682.08911.4
3.914.0410010.0781.85511.5
3.783.9110010.0931.8111.4
3.683.7810010.1051.68311.4
3.583.6810010.121.57611.5
3.493.5810010.1381.52411.4
3.413.4910010.1651.51511.5
3.343.4110010.181.44111.5
3.273.3410010.2251.47511.5
3.213.2710010.2721.40411.4
3.153.2110010.3161.41211.5
3.13.1510010.3651.39511.4
ReflectionResolution: 2.75→50 Å / Num. all: 24769 / Num. obs: 24596 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.9 % / Biso Wilson estimate: 69.1 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 16.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allDiffraction-ID% possible all
2.75-2.86.70.37112201100
2.8-2.858.10.29512381100
2.85-2.98.20.25912211100
2.9-2.968.20.20812271100
2.96-3.038.20.18112261100
3.03-3.18.20.16812141100
3.1-3.178.10.13412381100
3.17-3.268.20.11312151100
3.26-3.368.20.09612251100
3.36-3.468.20.08412621100
3.46-3.598.20.07212021100
3.59-3.738.20.06412551100
3.73-3.98.10.05812191100
3.9-4.118.20.05312431100
4.11-4.368.10.04912381100
4.36-4.78.10.04912291100
4.7-5.177.80.05612581100
5.17-5.927.20.05312461100
5.92-7.467.60.05112621100
7.46-507.30.0381158187.8

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
4
Phasing MADD res high: 3.1 Å / D res low: 1000 Å / FOM : 0.64 / Reflection: 18071
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
4 wavelength111.00611.64-15.22
4 wavelength121.00918.21-17.63
4 wavelength130.992911.21-9.39
4 wavelength141.005310.82-14.63
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Hg600.790.8760.3930.34
2Hg600.8070.6520.260.28
3Hg600.4790.6060.5250.138
4Hg600.5070.6260.5340.125
Phasing MAD shell
Resolution (Å)FOM Reflection
11.32-10000.85819
7.09-11.320.881485
5.53-7.090.821917
4.68-5.530.812244
4.13-4.680.762537
3.74-4.130.612798
3.44-3.740.473034
3.2-3.440.333237
Phasing dmFOM : 0.77 / FOM acentric: 0.77 / FOM centric: 0.71 / Reflection: 18025 / Reflection acentric: 16706 / Reflection centric: 1319
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8.9-37.820.980.980.96788648140
5.5-8.90.950.950.8824202163257
4.4-5.50.920.930.8230292793236
3.9-4.40.870.880.7430352830205
3.3-3.90.710.720.5454095100309
3.1-3.30.470.470.3333443172172

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
SOLVE2.13phasing
RESOLVE2.15phasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
PHENIX1.7.3_928phasing
RefinementMethod to determine structure: MAD / Resolution: 2.751→37.817 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7478 / SU ML: 0.46 / σ(F): 1.34 / Phase error: 30.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2751 1249 5.08 %RANDOM
Rwork0.2092 ---
all0.2125 24796 --
obs0.2125 24575 99.11 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.684 Å2 / ksol: 0.317 e/Å3
Displacement parametersBiso max: 214.99 Å2 / Biso mean: 88.3188 Å2 / Biso min: 30.98 Å2
Baniso -1Baniso -2Baniso -3
1--16.1474 Å2-0 Å20 Å2
2---16.1474 Å2-0 Å2
3---32.2949 Å2
Refinement stepCycle: LAST / Resolution: 2.751→37.817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4329 0 23 20 4372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084435
X-RAY DIFFRACTIONf_angle_d1.0886031
X-RAY DIFFRACTIONf_chiral_restr0.073707
X-RAY DIFFRACTIONf_plane_restr0.005777
X-RAY DIFFRACTIONf_dihedral_angle_d15.1221518
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7511-2.86120.38871250.31222543266898
2.8612-2.99140.37731420.261525842726100
2.9914-3.14910.32391530.240425882741100
3.1491-3.34620.30161330.229625832716100
3.3462-3.60440.27631340.209726112745100
3.6044-3.96680.25361540.205525802734100
3.9668-4.540.2271450.179226282773100
4.54-5.71670.23431330.181226422775100
5.7167-37.82020.30731300.21852567269794
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)
11.0415-0.3512-0.22970.6037-0.00030.3635-0.2463-0.1919-0.3809-0.1452-0.0625-0.24040.41490.21230.07630.38260.59430.37520.25640.27380.492431.181227.70135.0691
20.3194-1.04850.19673.5373-0.6240.1149-0.3447-0.4419-0.4030.7035-0.052-0.79720.17930.49030.14350.67830.19560.18580.6230.37080.867146.488452.147728.6144
30.01260.02530.02690.07650.05630.1097-0.1905-0.3452-0.3799-0.2393-0.0234-0.20130.34810.31210.11010.64270.40270.19210.46140.29480.812549.940336.622630.0977
41.0702-0.3180.24334.38810.11442.1586-0.04410.16220.4363-0.1557-0.12480.1335-0.1970.0290.14550.22870.0166-0.02620.29440.1270.5852-2.020471.060537.3361
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 102:258)A102 - 258
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 259:317)A259 - 317
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 318:418)A318 - 418
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 419:689)A419 - 689

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