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- PDB-8ixu: Rat Transcobalamin in Complex with Cobalamin -

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Basic information

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


Transport of RCbl within the body / cargo receptor ligand activity / cobalamin transport / cobalt ion 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 / NITRATE ION / Transcobalamin-2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)49,2259
Polymers47,6051
Non-polymers1,6198
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-52 kcal/mol
Surface area18220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.310, 54.530, 142.870
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

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 363 molecules

#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-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.24 Å3/Da / Density % sol: 45.03 % / Description: Clusters of arrow-shaped crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M NaNO3,20% PEG 3350, 0.1 M Bis-Tris propane pH 7.5

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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: 0.99 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jan 25, 2022
RadiationMonochromator: Si Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.3→48.29 Å / Num. obs: 99979 / % possible obs: 99.9 % / Redundancy: 13.2704567959 % / Biso Wilson estimate: 16.64 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.112 / Net I/σ(I): 13.58
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.3-1.333.1880.7472250.2773.3241
1.33-1.372.63171340.4432.7311
1.37-1.412.1731.2869400.5222.2561
1.41-1.451.741.6767390.6761.8061
1.45-1.51.3232.2865450.8041.3741
1.5-1.551.0512.9663470.8691.0911
1.55-1.610.8423.7961120.9080.8741
1.61-1.670.625.2158650.9480.6441
1.67-1.750.4986.4556700.9660.5171
1.75-1.830.3778.4454580.9780.3921
1.83-1.930.26711.4851360.9890.2791
1.93-2.050.1815.8249000.9940.1891
2.05-2.190.13321.3446370.9970.1391
2.19-2.370.10227.7842930.9980.1071
2.37-2.590.0834.6439910.9990.0831
2.59-2.90.06740.3336030.9990.0691
2.9-3.350.05148.2931990.9990.0531
3.35-4.10.03857.1127510.9990.041
4.1-5.80.03460.7421720.9990.0361
5.8-48.290.03157.75126210.0321

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Processing

Software
NameVersionClassification
PHENIX1.20-4459refinement
XDSJAN 10 2022data reduction
XSCALEJAN 10 2022data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→29.88 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.0292
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1714 1576 1.58 %
Rwork0.1603 98388 -
obs0.1605 99964 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.27 Å2
Refinement stepCycle: LAST / Resolution: 1.3→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3134 0 104 355 3593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613444
X-RAY DIFFRACTIONf_angle_d0.89644692
X-RAY DIFFRACTIONf_chiral_restr0.0658523
X-RAY DIFFRACTIONf_plane_restr0.0105622
X-RAY DIFFRACTIONf_dihedral_angle_d12.70451321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.340.34411510.33519633X-RAY DIFFRACTION99.35
1.34-1.40.30341560.30099731X-RAY DIFFRACTION100
1.4-1.460.26321560.2549744X-RAY DIFFRACTION99.98
1.46-1.540.24181590.2049726X-RAY DIFFRACTION99.95
1.54-1.630.19271550.17549795X-RAY DIFFRACTION100
1.63-1.760.1581650.15619804X-RAY DIFFRACTION100
1.76-1.940.18091490.14619823X-RAY DIFFRACTION100
1.94-2.220.16261610.13519869X-RAY DIFFRACTION99.98
2.22-2.790.15931610.14049955X-RAY DIFFRACTION99.99
2.79-29.880.14681630.149910308X-RAY DIFFRACTION99.98
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)
10.9748952798680.104454032680.2760897029331.050389004710.2538000139460.976168295244-0.0322799927685-0.04167741850660.0968758131969-0.110711192932-0.03329408338540.107489290992-0.0643593862205-0.09037224145850.01830523498810.1231688001490.00175154438592-0.0201629129340.124147040202-0.009748695211540.115408053853-9.336658470511.7104630889424.0323308354
21.439291034041.136728719522.296356410381.01594435462.004822022023.98865849124-0.028286626575-0.3077014538740.358381450067-0.232327959518-0.6490196113980.804004645889-0.429378653622-1.142100105610.6769114953280.989944048982-0.139125349692-0.1007604012051.35969527186-0.4086273364391.10929015772-0.653328757777-30.279060188712.4450259095
31.94421640330.4914099947040.4235997177211.993089371170.8024441242142.94098465110.035495053990.0354861639663-0.0181715533459-0.0076537015079-0.01557029129150.06899990409920.0454655610247-0.0417513885617-0.01589189266720.122944595406-0.00499763681503-0.01403870869840.127990254502-0.007022001377570.116044765107-14.8900990705-14.19744525772.0147604173
42.83446935036-0.004495343331830.9872687785472.021152250521.25230745294.06202110593-0.07348875570280.01300056543230.144623657183-0.0673674636899-0.02197896728620.00373913640183-0.128510979699-0.07396209191680.1165348822180.156590911725-0.00838050569461-0.02465926887210.132458918671-0.009476045353490.149772213796-13.2595689806-3.3764430841212.4364365503
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 19:322A19 - 3222 - 295
22chain A and resid 323:327A323 - 327296 - 300
33chain A and resid 328:427A328 - 427301 - 400
44chain A and resid 501B501

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