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- PDB-8ixt: Rat Transcobalamin in Complex with Glutathionylcobalamin -

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Basic information

Entry
Database: PDB / ID: 8ixt
TitleRat Transcobalamin in Complex with Glutathionylcobalamin
ComponentsTranscobalamin-2
KeywordsTRANSPORT PROTEIN / vitamin B12 / transporter / glutathione / alpha-6 barrel / ubiquitin-like
Function / homology
Function and homology information


Transport of RCbl within the body / cargo receptor ligand activity / cobalt ion transport / cobalamin transport / cobalamin binding / external side of plasma membrane / extracellular space / metal ion binding
Similarity search - Function
Domain of unknown function DUF4430 / Domain of unknown function (DUF4430) / Cobalamin (vitamin B12)-binding protein / Eukaryotic cobalamin-binding protein / Eukaryotic cobalamin-binding proteins signature.
Similarity search - Domain/homology
COBALAMIN / GLUTATHIONE / Transcobalamin-2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsBokhove, M. / Kumasaka, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP22ama121001 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101070 Japan
CitationJournal: J.Biol.Chem. / Year: 2024
Title: The structure of the rat vitamin B 12 transporter TC and its complex with glutathionylcobalamin.
Authors: Bokhove, M. / Kawamura, T. / Okumura, H. / Goto, S. / Kawano, Y. / Werner, S. / Jarczowski, F. / Klimyuk, V. / Saito, A. / Kumasaka, T.
History
DepositionApr 3, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcobalamin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3145
Polymers47,6051
Non-polymers1,7094
Water8,287460
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-40 kcal/mol
Surface area18380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.100, 55.060, 143.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Transcobalamin-2 / TC-2 / Transcobalamin II / TC II / TCII


Mass: 47605.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Tcn2 / Plasmid: MagnICON / Details (production host): pICK21104 / Production host: Nicotiana benthamiana (plant) / References: UniProt: Q9R0D6
#2: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Nonpolymer detailsGSH has a protonated amine (extra H13)

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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: 2.26 Å3/Da / Density % sol: 45.52 % / Description: Clusters of arrow-shaped crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 20 % PEG 3000 0.1M Sodium citrate pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: N2 cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 13, 2021
RadiationMonochromator: Si double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→37.5 Å / Num. obs: 127252 / % possible obs: 99.9 % / Redundancy: 43.7 % / Biso Wilson estimate: 13.08 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.09 / Rrim(I) all: 0.092 / Net I/σ(I): 22.44
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.2-1.231.772.2592130.7851.7981
1.23-1.261.4712.990730.851.4931
1.26-1.31.2343.5388330.8871.2521
1.3-1.341.074.1286260.9121.0861
1.34-1.390.8884.9683080.940.9021
1.39-1.430.7186.280470.9590.7281
1.43-1.490.5597.8878090.9780.5671
1.49-1.550.42610.1975100.9840.4321
1.55-1.620.33212.7572160.990.3371
1.62-1.70.2516.368890.9940.2541
1.7-1.790.19719.5465930.9960.21
1.79-1.90.14524.8562330.9970.1481
1.9-2.030.10334.6758740.9990.1051
2.03-2.190.0846.5354540.9990.0811
2.19-2.40.06754.6350510.9990.0681
2.4-2.680.05763.04461110.0571
2.68-3.10.04873.54406910.0481
3.1-3.790.04188.67348410.0411
3.79-5.370.03993.3275510.041
5.37-43.70.04284.5160410.0431

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Processing

Software
NameVersionClassification
PHENIX1.20-4459refinement
XDSJAN 10 2022data reduction
XSCALEJAN 10 2022data scaling
HKL2Map0.4.e-betaphasing
RefinementMethod to determine structure: SAD / Resolution: 1.2→37.45 Å / SU ML: 0.1019 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.0139
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1705 2016 1.58 %
Rwork0.1607 125222 -
obs0.1609 127238 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.66 Å2
Refinement stepCycle: LAST / Resolution: 1.2→37.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3141 0 113 460 3714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613378
X-RAY DIFFRACTIONf_angle_d0.99064602
X-RAY DIFFRACTIONf_chiral_restr0.0685517
X-RAY DIFFRACTIONf_plane_restr0.0129611
X-RAY DIFFRACTIONf_dihedral_angle_d12.07481306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.240.26092000.240212289X-RAY DIFFRACTION99.16
1.24-1.290.21512060.217112384X-RAY DIFFRACTION99.98
1.29-1.350.22591990.200912404X-RAY DIFFRACTION99.98
1.35-1.420.20291880.183512455X-RAY DIFFRACTION99.97
1.42-1.510.18392080.163212406X-RAY DIFFRACTION99.98
1.51-1.630.16741970.149412473X-RAY DIFFRACTION99.98
1.63-1.790.16642010.148712528X-RAY DIFFRACTION100
1.79-2.050.18652020.151512564X-RAY DIFFRACTION99.89
2.05-2.580.15292030.145112659X-RAY DIFFRACTION100
2.59-37.450.15652120.159913060X-RAY DIFFRACTION99.99
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)
10.87586345452-0.01954686237260.166610618510.9917475982590.1875751220690.660303620919-0.00843268047755-0.06293975948310.086635191172-0.0903654953025-0.04869625990450.108244119789-0.0501643684317-0.07091744020020.004950923222630.09298387064920.00815909925182-0.01706826567880.0951469554407-0.01478209838940.0833902736915-9.305428018721.9389917484824.3903913123
21.992692030622.037007560981.334090299552.237487294991.980803110693.34910401713-0.0241478458960.531212016058-0.610256297215-0.5443080931750.04337141209140.1747725821660.44852888811-0.1142816576130.07855551345660.4558112860740.00163431398636-0.08382663280770.302450554585-0.1099441620950.3794918909023.24138483878-22.04596343620.870658409
31.087510638710.6170686991970.5316237472631.585904968680.8374132983292.011796190410.02984713010040.0463685640091-0.02312344458530.0146872323968-0.02913481573560.07853316500970.012751634005-0.0441588928329-0.003763140250610.1162155492080.00977781837544-0.01394258606270.110405197414-0.01660819840640.11915556375-14.8215510757-14.08044705332.10548824681
41.48308528897-0.01206498682340.2080978925720.70097390580.5126440332161.53841786476-0.007010161770710.04623042578880.115142185695-0.0686767533179-0.0323381241657-0.023450893527-0.0916971534492-0.05196748675980.03991021520460.1458097108540.00539336432976-0.02077434415750.110984834225-0.01468986821210.127406219604-13.1064113635-3.4887723524112.5784062506
52.205144343550.126897043570.2695446520718.12575970422.201567827271.76626187669-0.102160971514-0.07317751489920.01786362937840.0270789085578-0.03553813161230.3747050680220.052536963355-0.08257407828910.117637735430.25286346650.0507984490424-0.05924080413140.192625826989-0.01640662732620.176757899778-19.9048853735-1.4617644463314.9961766577
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A

IDRefine TLS-IDSelection detailsLabel asym-IDAuth seq-IDLabel seq-ID
11chain A and resid 19:313A19 - 3135 - 287
22chain A and resid 314:328A314 - 328288 - 302
33chain A and resid 329:427A329 - 427303 - 401
44chain A and resid 501B501
55chain A and resid 502C502

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