[English] 日本語
Yorodumi
- PDB-8p0z: AP01-S2.3 - a variant of a redesigned transferrin receptor apical... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8p0z
TitleAP01-S2.3 - a variant of a redesigned transferrin receptor apical domain
ComponentsTransferrin receptor protein 1, serum form
KeywordsCYTOSOLIC PROTEIN / receptor domain / transferrin
Function / homology
Function and homology information


transferrin receptor activity / transferrin transport / negative regulation of mitochondrial fusion / Transferrin endocytosis and recycling / positive regulation of isotype switching / response to manganese ion / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / response to iron ion / response to copper ion / RND1 GTPase cycle ...transferrin receptor activity / transferrin transport / negative regulation of mitochondrial fusion / Transferrin endocytosis and recycling / positive regulation of isotype switching / response to manganese ion / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / response to iron ion / response to copper ion / RND1 GTPase cycle / RND2 GTPase cycle / Golgi Associated Vesicle Biogenesis / RHOB GTPase cycle / RHOC GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / RHOH GTPase cycle / transport across blood-brain barrier / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / positive regulation of bone resorption / RAC3 GTPase cycle / response to retinoic acid / positive regulation of T cell proliferation / clathrin-coated pit / positive regulation of B cell proliferation / RAC1 GTPase cycle / Hsp70 protein binding / osteoclast differentiation / response to nutrient / cellular response to leukemia inhibitory factor / acute-phase response / positive regulation of protein-containing complex assembly / clathrin-coated endocytic vesicle membrane / HFE-transferrin receptor complex / receptor internalization / recycling endosome / positive regulation of protein localization to nucleus / multicellular organismal-level iron ion homeostasis / recycling endosome membrane / double-stranded RNA binding / extracellular vesicle / melanosome / cellular response to xenobiotic stimulus / Cargo recognition for clathrin-mediated endocytosis / positive regulation of peptidyl-serine phosphorylation / Clathrin-mediated endocytosis / positive regulation of NF-kappaB transcription factor activity / virus receptor activity / iron ion transport / cytoplasmic vesicle / basolateral plasma membrane / positive regulation of canonical NF-kappaB signal transduction / intracellular iron ion homeostasis / blood microparticle / early endosome / response to hypoxia / endosome membrane / intracellular signal transduction / endosome / positive regulation of protein phosphorylation / external side of plasma membrane / intracellular membrane-bounded organelle / protein-containing complex binding / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / cell surface / protein homodimerization activity / RNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Transferrin receptor protein 1/2, PA domain / Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain superfamily / Glutamate carboxypeptidase 2-like / Transferrin receptor-like dimerisation domain / PA domain superfamily / PA domain / PA domain / Peptidase M28 / Peptidase family M28
Similarity search - Domain/homology
BORIC ACID / Transferrin receptor protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsOberdorfer, G. / Grill, B. / Bjelic, S. / Stoll, D.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)802217European Union
CitationJournal: J.Mol.Biol. / Year: 2023
Title: Affinity Maturated Transferrin Receptor Apical Domain Blocks Machupo Virus Glycoprotein Binding.
Authors: Sjostrom, D.J. / Grill, B. / Ambrosetti, E. / Veetil, A.A. / Mohlin, C. / Teixeira, A.I. / Oberdofer, G. / Bjelic, S.
History
DepositionMay 11, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transferrin receptor protein 1, serum form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2884
Polymers18,1811
Non-polymers1083
Water1,946108
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-21 kcal/mol
Surface area7980 Å2
Unit cell
Length a, b, c (Å)32.990, 57.370, 39.100
Angle α, β, γ (deg.)90.000, 113.152, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Transferrin receptor protein 1, serum form / sTfR


Mass: 18180.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TFRC / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21* (DE3) / References: UniProt: P02786
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BH3O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 34.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 11 mg/mL protein in 20 mM HEPES, pH 6.8, 150 mM NaCl mixed with 100 mM MIB buffer, pH 7.5, and 24 % PEG in a ratio 1:2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.88→35.95 Å / Num. obs: 10690 / % possible obs: 97.06 % / Redundancy: 4.2 % / Biso Wilson estimate: 30.96 Å2 / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.1036 / Rrim(I) all: 0.2192 / Net I/σ(I): 5.72
Reflection shellResolution: 1.88→1.947 Å / Rmerge(I) obs: 1.189 / Mean I/σ(I) obs: 0.75 / Num. unique obs: 1053 / CC1/2: 0.522 / CC star: 0.828 / Rpim(I) all: 0.6386 / Rrim(I) all: 1.356 / % possible all: 93.5

-
Processing

Software
NameVersionClassification
PHENIX1.18rc1_3777refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→35.95 Å / SU ML: 0.2548 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 30.3042
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2363 535 5.02 %random selection
Rwork0.2134 10130 --
obs0.2143 10664 97.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.35 Å2
Refinement stepCycle: LAST / Resolution: 1.88→35.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1176 0 6 108 1290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031290
X-RAY DIFFRACTIONf_angle_d0.64671751
X-RAY DIFFRACTIONf_chiral_restr0.0495203
X-RAY DIFFRACTIONf_plane_restr0.0025229
X-RAY DIFFRACTIONf_dihedral_angle_d13.4463484
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-2.070.32861320.3282497X-RAY DIFFRACTION95.84
2.07-2.370.2841330.25432511X-RAY DIFFRACTION97.35
2.37-2.980.2411330.22822534X-RAY DIFFRACTION97.23
2.98-35.950.20671370.17872588X-RAY DIFFRACTION97.92

+
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