[English] 日本語
Yorodumi
- PDB-2bb5: Structure of Human Transcobalamin in complex with Cobalamin -

+
Open data


ID or keywords:

Loading...

-
Basic information

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


Defective TCN2 causes TCN2 deficiency / Defective CD320 causes MMATC / Transport of RCbl within the body / cargo receptor ligand activity / cobalt ion transport / cobalamin transport / cobalamin binding / lysosomal lumen / external side of plasma membrane / extracellular space ...Defective TCN2 causes TCN2 deficiency / Defective CD320 causes MMATC / Transport of RCbl within the body / cargo receptor ligand activity / cobalt ion transport / cobalamin transport / 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 / Glycosyltransferase ...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
Remark 650HELIX DETERMINATION METHOD: AUTHOR PROVIDED
Remark 700SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

#1: Protein Transcobalamin II / Transcobalamin / 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 / Vitamin B12


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


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more