[English] 日本語
Yorodumi
- PDB-4zrp: TC:CD320 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zrp
TitleTC:CD320
Components
  • CD320 antigen
  • Transcobalamin-2
KeywordsTRANSPORT PROTEIN / LDLR-A / Vitamin transporter
Function / homology
Function and homology information


regulation of vitamin metabolic process / Defective TCN2 causes TCN2 deficiency / Defective CD320 causes MMATC / Transport of RCbl within the body / cargo receptor ligand activity / B cell costimulation / ventral spinal cord development / cobalt ion transport / cobalamin transport / cobalamin binding ...regulation of vitamin metabolic process / Defective TCN2 causes TCN2 deficiency / Defective CD320 causes MMATC / Transport of RCbl within the body / cargo receptor ligand activity / B cell costimulation / ventral spinal cord development / cobalt ion transport / cobalamin transport / cobalamin binding / cargo receptor activity / positive regulation of B cell proliferation / lysosomal lumen / caveola / growth factor activity / external side of plasma membrane / calcium ion binding / endoplasmic reticulum / extracellular space / extracellular region / membrane / 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 ...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 / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Beta Complex / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
CYANOCOBALAMIN / Transcobalamin-2 / CD320 antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAlam, A. / Locher, K.P.
CitationJournal: Nat Commun / Year: 2016
Title: Structural basis of transcobalamin recognition by human CD320 receptor.
Authors: Alam, A. / Woo, J.S. / Schmitz, J. / Prinz, B. / Root, K. / Chen, F. / Bloch, J.S. / Zenobi, R. / Locher, K.P.
History
DepositionMay 12, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Oct 10, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation_author / entity / entity_src_gen
Item: _citation_author.identifier_ORCID / _entity.formula_weight ..._citation_author.identifier_ORCID / _entity.formula_weight / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_vector_type
Revision 2.0Aug 25, 2021Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / database_PDB_caveat / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcobalamin-2
B: Transcobalamin-2
C: CD320 antigen
D: CD320 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,40918
Polymers116,9044
Non-polymers3,50614
Water7,999444
1
A: Transcobalamin-2
C: CD320 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,42912
Polymers58,4522
Non-polymers1,97710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-30 kcal/mol
Surface area22200 Å2
MethodPISA
2
B: Transcobalamin-2
D: CD320 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9806
Polymers58,4522
Non-polymers1,5294
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-16 kcal/mol
Surface area22620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.099, 98.099, 355.979
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
12chain C
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA0 - 409
211chain BB0 - 409
112chain CC53 - 170
212chain DD53 - 171

NCS ensembles :
ID
1
2

-
Components

-
Protein , 2 types, 4 molecules ABCD

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


Mass: 45650.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCN2, TC2 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P20062
#2: Protein CD320 antigen / 8D6 antigen / FDC-signaling molecule 8D6 / FDC-SM-8D6 / Transcobalamin receptor / TCblR


Mass: 12801.365 Da / Num. of mol.: 2 / Fragment: UNP residues 53-171
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD320, 8D6A, UNQ198/PRO224 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NPF0

-
Non-polymers , 4 types, 458 molecules

#3: Chemical ChemComp-CNC / CYANOCOBALAMIN


Mass: 1356.373 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C63H89CoN14O14P
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 444 / 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: 3.58 Å3/Da / Density % sol: 65.67 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: Calcium Acetate, MES, PEG8000

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→29.942 Å / Num. obs: 101389 / % possible obs: 98.97 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12
Reflection shellHighest resolution: 2.1 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1 / % possible all: 62.3

-
Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→29.942 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2075 1782 1.76 %
Rwork0.1836 99607 -
obs0.184 101389 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 188.04 Å2 / Biso mean: 58.5997 Å2 / Biso min: 21.28 Å2
Refinement stepCycle: final / Resolution: 2.1→29.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7515 0 42 444 8001
Biso mean--84.22 54.99 -
Num. residues----958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097740
X-RAY DIFFRACTIONf_angle_d1.92810535
X-RAY DIFFRACTIONf_chiral_restr0.1341185
X-RAY DIFFRACTIONf_plane_restr0.0071335
X-RAY DIFFRACTIONf_dihedral_angle_d13.5822820
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3700X-RAY DIFFRACTION8.918TORSIONAL
12B3700X-RAY DIFFRACTION8.918TORSIONAL
21C656X-RAY DIFFRACTION8.918TORSIONAL
22D656X-RAY DIFFRACTION8.918TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.15680.34611300.30827206733695
2.1568-2.22020.31311350.28437534766999
2.2202-2.29190.29011350.26487560769599
2.2919-2.37370.2821350.2397556769199
2.3737-2.46870.24171360.23267608774499
2.4687-2.5810.26931370.2157673781099
2.581-2.7170.23591360.207876237759100
2.717-2.88710.21391370.202776787815100
2.8871-3.10980.21991380.197976697807100
3.1098-3.42240.22281390.190277827921100
3.4224-3.91670.19761390.165278097948100
3.9167-4.9310.14631400.1397831797199
4.931-29.94540.18311450.15938078822398
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)
11.90230.6767-1.03170.9382-0.42912.19960.1531-0.15470.10660.1203-0.0882-0.0367-0.10090.0487-0.0520.39160.0139-0.00440.1762-0.02410.2601-30.0949-2.066-39.7
21.55810.8069-0.97131.7655-1.12613.6423-0.10310.0611-0.1062-0.25680.07180.00210.095-0.21360.03970.2586-0.01770.00670.3068-0.0660.2434-55.1127-20.4364-0.9216
37.33264.2389-0.07814.8593-0.10212.00230.3576-1.40333.08181.35080.07741.4781-2.1875-0.384-0.44881.23130.07790.32550.9286-0.23711.4878-52.902618.8423-27.0199
44.3441-2.64360.97022.01491.7436.3770.38890.2625-0.1358-0.58620.06321.5238-0.0534-1.8438-0.48650.5495-0.0267-0.06470.7340.05980.6189-62.853-8.2313-38.6155
58.41336.3809-0.74646.585-1.68279.3447-0.15441.63741.913-0.83450.85362.2388-1.0414-2.0169-0.6910.99270.2461-0.02051.240.31881.0798-70.29615.2018-16.6889
62.0103-0.48881.6499.3789-0.1274.70670.2184-0.46311.2107-0.18790.3461-0.4455-1.71650.3557-0.60620.9249-0.16290.10580.519-0.10560.4988-42.016410.3083-3.7257
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 409 )A0
2X-RAY DIFFRACTION2chain 'B' and (resid 0 through 409 )B0
3X-RAY DIFFRACTION3chain 'C' and (resid 53 through 89 )C0
4X-RAY DIFFRACTION4chain 'C' and (resid 130 through 171 )C0
5X-RAY DIFFRACTION5chain 'D' and (resid 53 through 89 )D0
6X-RAY DIFFRACTION6chain 'D' and (resid 130 through 171 )D0

+
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://pdbjlc1.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