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- PDB-8e6m: X-ray structure of the Deinococcus radiodurans Nramp/MntH divalen... -

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Basic information

Entry
Database: PDB / ID: 8e6m
TitleX-ray structure of the Deinococcus radiodurans Nramp/MntH divalent transition metal transporter WT in an inward-open, cadmium-bound state
ComponentsDivalent metal cation transporter MntH
KeywordsMETAL TRANSPORT / Membrane protein / divalent transition metal importer / LeuT fold / NRAMP family
Function / homology
Function and homology information


manganese ion transport / cadmium ion transmembrane transporter activity / manganese ion transmembrane transporter activity / iron ion transmembrane transport / symporter activity / metal ion binding / plasma membrane
Similarity search - Function
NRAMP family / Natural resistance-associated macrophage protein-like
Similarity search - Domain/homology
: / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / DI(HYDROXYETHYL)ETHER / Divalent metal cation transporter MntH
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsRay, S. / Gaudet, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM120996 United States
CitationJournal: Elife / Year: 2023
Title: High-resolution structures with bound Mn 2+ and Cd 2+ map the metal import pathway in an Nramp transporter.
Authors: Ray, S. / Berry, S.P. / Wilson, E.A. / Zhang, C.H. / Shekhar, M. / Singharoy, A. / Gaudet, R.
History
DepositionAug 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Mar 5, 2025Group: Data collection / Structure summary / Category: diffrn_detector / pdbx_entry_details
Item: _diffrn_detector.type / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Divalent metal cation transporter MntH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,10926
Polymers44,5771
Non-polymers7,53325
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, ITC shows micromolar affinity towards cadmium
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-30 kcal/mol
Surface area18980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.137, 71.369, 99.054
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Divalent metal cation transporter MntH


Mass: 44576.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: mntH, DR_1709 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RTP8

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Non-polymers , 5 types, 79 molecules

#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.35 Å3/Da / Density % sol: 47.59 % / Description: 35 micron in size
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 6.1
Details: 24% PEG400, 0.1 M MES, pH 6.1, 50 mM succinic acid, pH 6.0, 20 mM spermidine, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.48→45.54 Å / Num. obs: 15312 / % possible obs: 99.4 % / Redundancy: 4.9 % / Biso Wilson estimate: 49.52 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.083 / Rrim(I) all: 0.184 / Net I/σ(I): 8.1 / Num. measured all: 74940 / Scaling rejects: 47
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.48-2.584.81.626819616970.3670.8231.8311.199.7
8.94-45.544.30.02815703650.9990.0140.03231.496.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 8E5S

8e5s


Resolution: 2.48→45.54 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2504 2786 9.97 %
Rwork0.2029 25154 -
obs0.2077 15291 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 187.83 Å2 / Biso mean: 64.8177 Å2 / Biso min: 27.63 Å2
Refinement stepCycle: final / Resolution: 2.48→45.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2905 0 362 54 3321
Biso mean--83.11 57.45 -
Num. residues----388
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.48-2.520.34561340.32531224135896
2.52-2.570.35971360.31341276141297
2.57-2.620.34241420.30031273141599
2.62-2.670.32591410.30541267140898
2.67-2.730.3991370.30221277141499
2.73-2.790.36841330.28941245137898
2.79-2.860.32841380.27681284142297
2.86-2.940.31241410.25671257139898
2.94-3.030.28421370.26311269140698
3.03-3.120.33161470.24371288143598
3.12-3.240.32261420.22791241138398
3.24-3.370.24391410.20971253139498
3.37-3.520.22741410.1941292143399
3.52-3.70.28281440.16881286143098
3.7-3.940.21191450.16211248139398
3.94-4.240.17411460.15521248139496
4.24-4.670.22531380.16431222136095
4.67-5.340.23381380.17981215135395
5.34-6.720.22441350.19611254138997
6.73-45.540.19141300.16721235136595
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)
11.02220.05880.35561.2077-0.6521.7865-0.0063-0.0127-0.059-0.1921-0.064-0.08050.1180.08820.0740.30380.04780.03250.26490.00040.3377-12.992-20.32424.2272
22.87460.96071.78971.05850.68771.1256-0.03670.7274-0.279-0.87960.2428-0.33181.28120.4344-0.33770.871-0.0849-0.03880.52640.03960.5307-16.9087-18.546311.3393
31.1006-0.05280.52591.5248-0.72532.3266-0.0507-0.0679-0.0389-0.1021-0.006-0.00460.0165-0.01510.05740.2530.04340.02820.2516-0.00870.3107-15.4253-17.644323.0783
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 41 through 228 )A41 - 228
2X-RAY DIFFRACTION2chain 'A' and (resid 229 through 249 )A229 - 249
3X-RAY DIFFRACTION3chain 'A' and (resid 250 through 436 )A250 - 436

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