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- PDB-2bb5: Structure of Human Transcobalamin in complex with Cobalamin -

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Basic information

Entry
Database: PDB / ID: 2bb5
TitleStructure of Human Transcobalamin in complex with Cobalamin
ComponentsTranscobalamin II
KeywordsTRANSPORT PROTEIN / alpha_6 - alpha_6 barrel
Function / homology
Function and homology information


Defective TCN2 causes TCN2 deficiency / Defective CD320 causes MMATC / cargo receptor ligand activity / Transport of RCbl within the body / cobalamin transport / cobalt ion transport / molecular carrier activity / cobalamin binding / lysosomal lumen / external side of plasma membrane ...Defective TCN2 causes TCN2 deficiency / Defective CD320 causes MMATC / cargo receptor ligand activity / Transport of RCbl within the body / cobalamin transport / cobalt ion transport / molecular carrier activity / cobalamin binding / lysosomal lumen / external side of plasma membrane / extracellular space / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
Ferric Hydroxamate Uptake Protein; Chain A, domain 1 - #30 / Domain of unknown function DUF4430 / Domain of unknown function (DUF4430) / Cobalamin (vitamin B12)-binding protein / : / Eukaryotic cobalamin-binding protein / Eukaryotic cobalamin-binding proteins signature. / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / Glycosyltransferase - #20 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid ...Ferric Hydroxamate Uptake Protein; Chain A, domain 1 - #30 / Domain of unknown function DUF4430 / Domain of unknown function (DUF4430) / Cobalamin (vitamin B12)-binding protein / : / Eukaryotic cobalamin-binding protein / Eukaryotic cobalamin-binding proteins signature. / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / Glycosyltransferase - #20 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Beta Complex / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
COBALAMIN / Transcobalamin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsWuerges, J. / Garau, G. / Geremia, S. / Fedosov, S.N. / Petersen, T.E. / Randaccio, L.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Structural basis for mammalian vitamin B12 transport by transcobalamin.
Authors: Wuerges, J. / Garau, G. / Geremia, S. / Fedosov, S.N. / Petersen, T.E. / Randaccio, L.
History
DepositionOct 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 24, 2012Group: Non-polymer description
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 650HELIX DETERMINATION METHOD: AUTHOR PROVIDED
Remark 700SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcobalamin II
B: Transcobalamin II
A: COBALAMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9004
Polymers91,2392
Non-polymers2,6612
Water1448
1
A: Transcobalamin II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9502
Polymers45,6191
Non-polymers1,3301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transcobalamin II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9502
Polymers45,6191
Non-polymers1,3301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.127, 145.497, 165.043
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
151A
161B
171A
181B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUGLUGLU2AA1 - 71 - 7
21GLUGLUGLUGLU2BB1 - 71 - 7
32METMETGLYGLY1AA8 - 688 - 68
42METMETGLYGLY1BB8 - 688 - 68
53SERSERGLNGLN6AA69 - 7969 - 79
63SERSERGLNGLN6BB69 - 7969 - 79
74GLYGLYPHEPHE1AA80 - 16880 - 168
84GLYGLYPHEPHE1BB80 - 16880 - 168
95HISHISHISHIS4AA169 - 173169 - 173
105HISHISHISHIS4BB169 - 173169 - 173
116SERSERALAALA1AA174 - 301174 - 301
126SERSERALAALA1BB174 - 301174 - 301
137ALAALAGLNGLN6AA302 - 307302 - 307
147ALAALAGLNGLN6BB302 - 307302 - 307
158THRTHRSERSER4AA308 - 313308 - 313
168THRTHRSERSER4BB308 - 313308 - 313
179VALVALTRPTRP1AA314 - 409314 - 409
189VALVALTRPTRP1BB314 - 409314 - 409

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Components

#1: Protein Transcobalamin II / TCII / TC II


Mass: 45619.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCN2, TC2 / Production host: Pichia pastoris (fungus) / Strain (production host): SMD 1168 / References: UniProt: P20062
#2: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
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: 3.23 Å3/Da / Density % sol: 61.93 %
Crystal growTemperature: 293 K / pH: 7.6
Details: 20% PEG 4000, 18% ethanol, 0.2M TRIS, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2
DetectorType: MARRESEARCH / Detector: CCD / Date: May 14, 2001
RadiationMonochromator: DOUBLE CRYSTAL (SI111, SI220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 3.2→29.24 Å / Num. obs: 19417 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.142 / Rsym value: 0.142 / Net I/σ(I): 4.5
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.388 / % possible all: 95.5

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT1.7data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: STRUCTURE OF BOVINE TRANSCOBALAMIN IN MONOCLINIC CRYSTAL FORM (PDB 2BB6).

2bb6


Resolution: 3.2→20 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.889 / SU B: 57.692 / SU ML: 0.457 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.571 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS,ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.288 997 5.2 %RANDOM
Rwork0.257 ---
obs0.258 19334 95.6 %-
all-19334 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.46 Å2
Baniso -1Baniso -2Baniso -3
1--2.42 Å20 Å20 Å2
2--4.91 Å20 Å2
3----2.49 Å2
Refinement stepCycle: LAST / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6406 0 182 8 6596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0216756
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0942.0169232
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6115816
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.09523.873284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.765151136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7011540
X-RAY DIFFRACTIONr_chiral_restr0.070.21024
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025100
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.23210
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.24620
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2205
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.272
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3570.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3921.54074
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.72126546
X-RAY DIFFRACTIONr_scbond_it0.56932682
X-RAY DIFFRACTIONr_scangle_it0.9844.52686
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
2958tight positional0.020.05
118medium positional0.530.5
125loose positional1.295
2958tight thermal0.020.5
118medium thermal0.272
125loose thermal0.7210
LS refinement shellResolution: 3.2→3.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 81 -
Rwork0.369 1290 -
obs--93.84 %
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)
10.0303-0.0042-0.03510.0430.07630.16110.1629-0.04160.0384-0.362-0.14050.00920.17540.0229-0.02240.0002-0.00020.00010-0.0001036.869336.353518.3453
21.0266-1.46510.61812.3214-0.93860.58410.0350.02120.00720.0132-0.071-0.0351-0.01740.0270.036-0.0741-0.05630.0473-0.0084-0.0266-0.093936.841336.323129.863
30.1489-0.31810.23040.6798-0.49230.3565-0.048-0.01970.0242-0.04480.0747-0.05370.0577-0.0518-0.0267-0.00180.03760.0324-0.00930.0541-0.021236.83736.27579.4881
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC01
2X-RAY DIFFRACTION1BD4101
3X-RAY DIFFRACTION2AA1 - 3001 - 300
4X-RAY DIFFRACTION2BB1 - 3001 - 300
5X-RAY DIFFRACTION3AA313 - 409313 - 409
6X-RAY DIFFRACTION3BB313 - 409313 - 409

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