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- PDB-7qji: X-Ray Structure of apo-EleNRMT in complex with two Nanobodies at 4.1A -

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Basic information

Entry
Database: PDB / ID: 7qji
TitleX-Ray Structure of apo-EleNRMT in complex with two Nanobodies at 4.1A
Components
  • (Elen-Nanobody-complex) x 2
  • Divalent metal cation transporter
KeywordsMEMBRANE PROTEIN / SLC11 / NRAMP-related Mg2+ transporter / Nanobody complex
Function / homologyNRAMP family / Natural resistance-associated macrophage protein-like / cadmium ion transmembrane transporter activity / manganese ion transmembrane transporter activity / iron ion transmembrane transport / plasma membrane / Divalent metal cation transporter
Function and homology information
Biological speciesVicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1 Å
AuthorsRamanadane, K. / Straub, M.S. / Dutzler, R. / Manatschal, C.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Elife / Year: 2022
Title: Structural and functional properties of a magnesium transporter of the SLC11/NRAMP family.
Authors: Karthik Ramanadane / Monique S Straub / Raimund Dutzler / Cristina Manatschal /
Abstract: Members of the ubiquitous SLC11/NRAMP family catalyze the uptake of divalent transition metal ions into cells. They have evolved to efficiently select these trace elements from a large pool of Ca and ...Members of the ubiquitous SLC11/NRAMP family catalyze the uptake of divalent transition metal ions into cells. They have evolved to efficiently select these trace elements from a large pool of Ca and Mg, which are both orders of magnitude more abundant, and to concentrate them in the cytoplasm aided by the cotransport of H serving as energy source. In the present study, we have characterized a member of a distant clade of the family found in prokaryotes, termed NRMTs, that were proposed to function as transporters of Mg. The protein transports Mg and Mn but not Ca by a mechanism that is not coupled to H. Structures determined by cryo-EM and X-ray crystallography revealed a generally similar protein architecture compared to classical NRAMPs, with a restructured ion binding site whose increased volume provides suitable interactions with ions that likely have retained much of their hydration shell.
History
DepositionDec 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Divalent metal cation transporter
C: Elen-Nanobody-complex
B: Elen-Nanobody-complex
E: Divalent metal cation transporter
F: Elen-Nanobody-complex
G: Elen-Nanobody-complex


Theoretical massNumber of molelcules
Total (without water)146,3076
Polymers146,3076
Non-polymers00
Water00
1
A: Divalent metal cation transporter
C: Elen-Nanobody-complex
B: Elen-Nanobody-complex


Theoretical massNumber of molelcules
Total (without water)73,1533
Polymers73,1533
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Divalent metal cation transporter
F: Elen-Nanobody-complex
G: Elen-Nanobody-complex


Theoretical massNumber of molelcules
Total (without water)73,1533
Polymers73,1533
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.270, 122.250, 149.110
Angle α, β, γ (deg.)90.000, 107.794, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "E"
d_1ens_2chain "B"
d_2ens_2chain "G"
d_1ens_3chain "C"
d_2ens_3chain "F"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAILEA1 - 398
d_21ens_1ALAILED1 - 398
d_11ens_2GLNVALC1 - 121
d_21ens_2GLNVALF1 - 121
d_11ens_3GLNVALB1 - 117
d_21ens_3GLNVALE1 - 117

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.999822124177, -0.00509489058152, 0.0181593528718), (0.00455555209282, -0.999550882107, -0.0296189301761), (0.0183021023899, -0.0295309358065, 0.99939629621)-46.7308084687, -39.9578248565, -36.9872237687
2given(-0.999873607687, 0.00348463715053, 0.0155121228149), (-0.00412651066162, -0.999128277338, -0.0415410319224), (0.0153538451228, -0.0415997923955, 0.999016374597)-46.395898669, -40.3784149664, -37.6636689545
3given(-0.999951558665, 0.00399814690557, -0.00899417279594), (-0.00368360594478, -0.99939027519, -0.0347204392559), (-0.00912750624242, -0.0346856263631, 0.999356590989)-46.4793028513, -39.9964845611, -38.0083119818

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Components

#1: Protein Divalent metal cation transporter


Mass: 46848.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Gene: C1853_09580, C1871_08405 / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: A0A369N1S1
#2: Antibody Elen-Nanobody-complex


Mass: 12952.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Gene: C1867_11315 / Production host: Escherichia coli MC1061 (bacteria)
#3: Antibody Elen-Nanobody-complex


Mass: 13351.896 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Gene: C1867_11315 / Production host: Escherichia coli MC1061 (bacteria)
Has protein modificationY

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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: 2.75 Å3/Da / Density % sol: 55.24 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 50 mM MgAc, 50 mM HEPES pH 7.2-7.6 and 25-30% PEG400

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999869 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999869 Å / Relative weight: 1
ReflectionResolution: 4.1→12 Å / Num. obs: 25065 / % possible obs: 99.2 % / Redundancy: 28.2 % / Biso Wilson estimate: 174.298 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.112 / Net I/σ(I): 15.36
Reflection shellResolution: 4.1→4.2 Å / Redundancy: 27.1 % / Mean I/σ(I) obs: 1.81 / Num. unique obs: 1742 / CC1/2: 0.95 / Rrim(I) all: 1.536 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158phasing
PHENIX1.19.2_4158refinement
XDSVersion Feb5 2021data reduction
Coot0.9.6model building
XSCALEVersion Feb5 2021data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 7QIA

7qia


Resolution: 4.1→11.99 Å / SU ML: 0.4077 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 43.327
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3155 1136 4.79 %
Rwork0.2669 22603 -
obs0.2693 23739 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 287.33 Å2
Refinement stepCycle: LAST / Resolution: 4.1→11.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9632 0 0 0 9632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00299836
X-RAY DIFFRACTIONf_angle_d0.603413376
X-RAY DIFFRACTIONf_chiral_restr0.0431578
X-RAY DIFFRACTIONf_plane_restr0.00481668
X-RAY DIFFRACTIONf_dihedral_angle_d12.90443416
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONcartesian NCS0.00121269570318
ens_2d_2CX-RAY DIFFRACTIONcartesian NCS0.00122716768505
ens_3d_2BX-RAY DIFFRACTIONcartesian NCS0.00122046365699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.1-4.280.43221430.33432846X-RAY DIFFRACTION98.39
4.28-4.490.37321610.27772777X-RAY DIFFRACTION98.16
4.49-4.760.34271160.28042815X-RAY DIFFRACTION97.96
4.76-5.10.34871470.2692806X-RAY DIFFRACTION97.49
5.1-5.560.37471500.28142786X-RAY DIFFRACTION97.22
5.57-6.270.44011310.29692804X-RAY DIFFRACTION97.67
6.27-7.550.2911230.29792902X-RAY DIFFRACTION99.7
7.55-11.990.25351650.22652867X-RAY DIFFRACTION98.86
Refinement TLS params.Method: refined / Origin x: -23.4158834813 Å / Origin y: -19.9665088173 Å / Origin z: -30.6155185713 Å
111213212223313233
T2.58621080997 Å20.292731382921 Å2-0.0667267579602 Å2-2.97775752703 Å2-0.119734171616 Å2--2.05052313074 Å2
L0.891836388223 °21.03277170841 °2-0.636109869841 °2-1.79916815361 °2-1.25805303135 °2--0.763021659379 °2
S-0.197744281364 Å °0.370525769045 Å °0.0461154452735 Å °-0.641057260731 Å °0.143316320303 Å °0.0666581459335 Å °0.454913689261 Å °0.0953929252043 Å °0.0678192737815 Å °
Refinement TLS groupSelection details: all

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