[English] 日本語
Yorodumi
- PDB-6uj6: X-ray Crystal Structure of Chromium-transferrin with Synergistic ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6uj6
TitleX-ray Crystal Structure of Chromium-transferrin with Synergistic Anion Malonate
ComponentsTransferrin
KeywordsMETAL TRANSPORT / chromium / transferrin / human
Function / homology
Function and homology information


iron chaperone activity / Transferrin endocytosis and recycling / transferrin receptor binding / dense body / basal part of cell / positive regulation of cell motility / endocytic vesicle / positive regulation of bone resorption / clathrin-coated pit / positive regulation of phosphorylation ...iron chaperone activity / Transferrin endocytosis and recycling / transferrin receptor binding / dense body / basal part of cell / positive regulation of cell motility / endocytic vesicle / positive regulation of bone resorption / clathrin-coated pit / positive regulation of phosphorylation / ERK1 and ERK2 cascade / ferric iron binding / osteoclast differentiation / basal plasma membrane / cellular response to iron ion / actin filament organization / Iron uptake and transport / Post-translational protein phosphorylation / clathrin-coated endocytic vesicle membrane / regulation of protein stability / ferrous iron binding / regulation of iron ion transport / HFE-transferrin receptor complex / recycling endosome / positive regulation of receptor-mediated endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Cargo recognition for clathrin-mediated endocytosis / late endosome / Platelet degranulation / Clathrin-mediated endocytosis / iron ion transport / antibacterial humoral response / cytoplasmic vesicle / secretory granule lumen / intracellular iron ion homeostasis / vesicle / early endosome / blood microparticle / endosome membrane / apical plasma membrane / endoplasmic reticulum lumen / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / cell surface / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Serotransferrin, mammalian / Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin-like domain / Transferrin / Transferrin / Transferrin-like domain profile. / Transferrin
Similarity search - Domain/homology
BICARBONATE ION / CHROMIUM ION / MALONATE ION / Serotransferrin / Beta-1 metal-binding globulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsPetersen, C.M. / Edwards, K.C. / Gilbert, N.C. / Vincent, J.B. / Thompson, M.K.
CitationJournal: J.Inorg.Biochem. / Year: 2020
Title: X-ray structure of chromium(III)-containing transferrin: First structure of a physiological Cr(III)-binding protein.
Authors: Petersen, C.M. / Edwards, K.C. / Gilbert, N.C. / Vincent, J.B. / Thompson, M.K.
History
DepositionOct 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4636
Polymers77,0641
Non-polymers3995
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)137.046, 158.031, 107.136
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Transferrin


Mass: 77063.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q06AH7, UniProt: P02787*PLUS

-
Non-polymers , 5 types, 39 molecules

#2: Chemical ChemComp-CR / CHROMIUM ION


Mass: 51.996 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cr / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.76 Å3/Da / Density % sol: 67.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: HEPES, disodium malonate, PEG 3350, glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 1.38 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38 Å / Relative weight: 1
ReflectionResolution: 2.67→50 Å / Num. obs: 32784 / % possible obs: 97.4 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.221 / Rpim(I) all: 0.088 / Rrim(I) all: 0.238 / Χ2: 1.214 / Net I/σ(I): 5.4 / Num. measured all: 225779
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.67-2.774.90.67725110.6410.3130.750.68575.4
2.77-2.886.30.74732850.8180.3150.8120.5599.1
2.88-3.0170.55333230.9270.2220.5960.46399.9
3.01-3.177.20.38233240.9540.1520.4110.47699.9
3.17-3.367.20.23233290.9830.0920.250.515100
3.36-3.627.20.46333600.9740.1820.4982.373100
3.62-3.997.20.46433520.9880.1850.53.118100
3.99-4.567.20.07333630.9970.0290.0780.744100
4.56-5.757.20.05934070.9980.0240.0640.737100
5.75-506.90.0535300.9970.0210.0542.05999.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QYT

3qyt


Resolution: 2.68→49.22 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.9 / SU B: 0.003 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.243 / ESU R Free: 0.298
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2702 1545 4.7 %RANDOM
Rwork0.22 ---
obs0.2224 31209 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 150.91 Å2 / Biso mean: 58.979 Å2 / Biso min: 24.27 Å2
Baniso -1Baniso -2Baniso -3
1-4.94 Å20 Å20 Å2
2---1.49 Å20 Å2
3----3.46 Å2
Refinement stepCycle: final / Resolution: 2.68→49.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5029 0 24 34 5087
Biso mean--59.29 37.1 -
Num. residues----652
LS refinement shellResolution: 2.68→2.746 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.403 83 -
Rwork0.384 2024 -
obs--87.94 %

+
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://pdbjlvh1.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