[English] 日本語
Yorodumi
- PDB-3fgs: Crystal structure of G65R/K206E double mutant of the N-lobe human... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fgs
TitleCrystal structure of G65R/K206E double mutant of the N-lobe human transferrin
ComponentsSerotransferrin
KeywordsMETAL TRANSPORT / Human transferrin / Iron binding protein / Dilysine pair / Disease mutation / Glycoprotein / Ion transport / Iron / Iron transport / Metal-binding / Methylation / Phosphoprotein / Polymorphism / Secreted / Transport
Function / homology
Function and homology information


iron chaperone activity / Transferrin endocytosis and recycling / transferrin receptor binding / basal part of cell / positive regulation of cell motility / endocytic vesicle / positive regulation of bone resorption / positive regulation of phosphorylation / clathrin-coated pit / ERK1 and ERK2 cascade ...iron chaperone activity / Transferrin endocytosis and recycling / transferrin receptor binding / basal part of cell / positive regulation of cell motility / endocytic vesicle / positive regulation of bone resorption / positive regulation of phosphorylation / clathrin-coated pit / ERK1 and ERK2 cascade / ferric iron binding / osteoclast differentiation / basal plasma membrane / actin filament organization / cellular response to iron ion / Post-translational protein phosphorylation / Iron uptake and transport / clathrin-coated endocytic vesicle membrane / ferrous iron binding / regulation of iron ion transport / regulation of protein stability / HFE-transferrin receptor complex / recycling endosome / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / late endosome / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Cargo recognition for clathrin-mediated endocytosis / Platelet degranulation / antibacterial humoral response / Clathrin-mediated endocytosis / iron ion transport / cytoplasmic vesicle / secretory granule lumen / intracellular iron ion homeostasis / vesicle / blood microparticle / transmembrane transporter binding / early endosome / endosome membrane / apical plasma membrane / endoplasmic reticulum lumen / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / enzyme binding / 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 ...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 / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CARBONATE ION / : / Serotransferrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsHalbrooks, P.J. / Mason, A.B. / Everse, S.J.
CitationJournal: Biochemistry / Year: 2009
Title: Structural and Functional Consequences of the Substitution of Glycine 65 with Arginine in the N-Lobe of Human Transferrin.
Authors: Mason, A.B. / Halbrooks, P.J. / James, N.G. / Byrne, S.L. / Grady, J.K. / Chasteen, N.D. / Bobst, C.E. / Kaltashov, I.A. / Smith, V.C. / Macgillivray, R.T. / Everse, S.J.
History
DepositionDec 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4313
Polymers37,3151
Non-polymers1162
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.347, 57.056, 133.737
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Serotransferrin / Transferrin / Siderophilin / Beta-1-metal-binding globulin


Mass: 37315.344 Da / Num. of mol.: 1 / Fragment: Peptidase S60 1 domain / Mutation: G65R, K206E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRO1400, TF, transferrin / Plasmid: pNUT / Production host: Mesocricetus auratus (golden hamster) / Strain (production host): BHK / References: UniProt: P02787
#2: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 200 mM potassium acetate buffer (pH 7.7) containing 10 mM KCl and 18% polyethylene glycol 3350. Concentration of the mutant was 17.5 mg/mL. Crystals appeared in approximately a week ...Details: 200 mM potassium acetate buffer (pH 7.7) containing 10 mM KCl and 18% polyethylene glycol 3350. Concentration of the mutant was 17.5 mg/mL. Crystals appeared in approximately a week following micro-seeding with wild-type N-lobe, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 7, 2001 / Details: Xenocs FOX-2D Multilayer Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 29637 / % possible obs: 93.3 % / Rmerge(I) obs: 0.049 / Χ2: 1.511
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.860.11327011.94987.2
1.86-1.940.0928191.92790.3
1.94-2.030.07728631.75391.9
2.03-2.130.07429081.8492.7
2.13-2.270.06229761.71394.4
2.27-2.440.05529991.49795.2
2.44-2.690.05230301.41595.9
2.69-3.080.04730891.31896.7
3.08-3.880.04331341.11297
3.88-300.04231181.09791.4

-
Phasing

PhasingMethod: molecular replacement
Phasing MRMethod rotation: fast direct / Method translation: &STRIP%trans_method

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.49 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.246 2976 9.4 %
Rwork0.216 --
obs-29542 93.6 %
Solvent computationBsol: 36.137 Å2
Displacement parametersBiso max: 45.94 Å2 / Biso mean: 14.999 Å2 / Biso min: 5.79 Å2
Baniso -1Baniso -2Baniso -3
1--1.057 Å20 Å20 Å2
2--0.768 Å20 Å2
3---0.288 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2557 0 5 269 2831
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it0.761.5
X-RAY DIFFRACTIONc_scbond_it1.2522
X-RAY DIFFRACTIONc_mcangle_it1.1922
X-RAY DIFFRACTIONc_scangle_it1.8522.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3fe3.param
X-RAY DIFFRACTION4co3.param

+
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