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- PDB-3s9l: Complex between transferrin receptor 1 and transferrin with iron ... -

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Basic information

Entry
Database: PDB / ID: 3s9l
TitleComplex between transferrin receptor 1 and transferrin with iron in the N-Lobe, cryocooled 2
Components
  • Serotransferrin
  • Transferrin receptor protein 1
KeywordsTRANSPORT PROTEIN / Transferrin receptor complex / transferrin superfamily / carboxypeptidase like
Function / homology
Function and homology information


transferrin receptor activity / negative regulation of mitochondrial fusion / transferrin transport / iron chaperone activity / Transferrin endocytosis and recycling / transferrin receptor binding / positive regulation of isotype switching / basal part of cell / positive regulation of cell motility / response to iron ion ...transferrin receptor activity / negative regulation of mitochondrial fusion / transferrin transport / iron chaperone activity / Transferrin endocytosis and recycling / transferrin receptor binding / positive regulation of isotype switching / basal part of cell / positive regulation of cell motility / response to iron ion / response to copper ion / response to manganese ion / RND1 GTPase cycle / RND2 GTPase cycle / RHOB GTPase cycle / Golgi Associated Vesicle Biogenesis / RHOJ GTPase cycle / RHOC GTPase cycle / RHOQ GTPase cycle / RHOH GTPase cycle / CDC42 GTPase cycle / transport across blood-brain barrier / endocytic vesicle / RHOG GTPase cycle / RHOA GTPase cycle / RAC3 GTPase cycle / RAC2 GTPase cycle / positive regulation of bone resorption / response to retinoic acid / positive regulation of B cell proliferation / clathrin-coated pit / positive regulation of phosphorylation / ERK1 and ERK2 cascade / Hsp70 protein binding / positive regulation of T cell proliferation / RAC1 GTPase cycle / cellular response to leukemia inhibitory factor / basal plasma membrane / ferric iron binding / osteoclast differentiation / response to nutrient / actin filament organization / Post-translational protein phosphorylation / acute-phase response / positive regulation of protein-containing complex assembly / ferrous iron binding / clathrin-coated endocytic vesicle membrane / Iron uptake and transport / regulation of protein stability / regulation of iron ion transport / receptor internalization / HFE-transferrin receptor complex / cellular response to iron ion / recycling endosome / positive regulation of receptor-mediated endocytosis / positive regulation of protein localization to nucleus / recycling endosome membrane / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / extracellular vesicle / melanosome / cellular response to xenobiotic stimulus / double-stranded RNA binding / late endosome / Cargo recognition for clathrin-mediated endocytosis / Platelet degranulation / virus receptor activity / Clathrin-mediated endocytosis / positive regulation of peptidyl-serine phosphorylation / positive regulation of NF-kappaB transcription factor activity / antibacterial humoral response / iron ion transport / cytoplasmic vesicle / basolateral plasma membrane / blood microparticle / positive regulation of canonical NF-kappaB signal transduction / secretory granule lumen / intracellular iron ion homeostasis / vesicle / response to hypoxia / early endosome / endosome membrane / endosome / intracellular signal transduction / positive regulation of protein phosphorylation / apical plasma membrane / endoplasmic reticulum lumen / 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 / positive regulation of DNA-templated transcription / cell surface / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome / extracellular region
Similarity search - Function
Transferrin receptor protein 1/2, PA domain / Serotransferrin, mammalian / Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain superfamily / Glutamate carboxypeptidase 2-like / Transferrin receptor-like dimerisation domain / Glucose Oxidase; domain 1 - #30 / PA domain superfamily / PA domain ...Transferrin receptor protein 1/2, PA domain / Serotransferrin, mammalian / Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain superfamily / Glutamate carboxypeptidase 2-like / Transferrin receptor-like dimerisation domain / Glucose Oxidase; domain 1 - #30 / PA domain superfamily / PA domain / PA domain / Transcription Elongation Factor S-II; Chain A / 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 / Glucose Oxidase; domain 1 / Peptidase M28 / Peptidase family M28 / Zn peptidases / Aminopeptidase / Periplasmic binding protein-like II / 3-Layer(bba) Sandwich / D-Maltodextrin-Binding Protein; domain 2 / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CARBONATE ION / : / Transferrin receptor protein 1 / Serotransferrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 3.22 Å
AuthorsEckenroth, B.E. / Steere, A.N. / Mason, A.B. / Everse, S.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: How the binding of human transferrin primes the transferrin receptor potentiating iron release at endosomal pH.
Authors: Eckenroth, B.E. / Steere, A.N. / Chasteen, N.D. / Everse, S.J. / Mason, A.B.
History
DepositionJun 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2011Group: Derived calculations / Other
Revision 1.2Dec 14, 2011Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transferrin receptor protein 1
B: Transferrin receptor protein 1
C: Serotransferrin
D: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)301,78112
Polymers301,0274
Non-polymers7548
Water0
1
A: Transferrin receptor protein 1
C: Serotransferrin
hetero molecules

A: Transferrin receptor protein 1
C: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)301,78112
Polymers301,0274
Non-polymers7548
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+1,y,-z1
Buried area3400 Å2
ΔGint-24 kcal/mol
Surface area46670 Å2
2
B: Transferrin receptor protein 1
D: Serotransferrin
hetero molecules

B: Transferrin receptor protein 1
D: Serotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)301,78112
Polymers301,0274
Non-polymers7548
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-3/41
Buried area3290 Å2
ΔGint-27 kcal/mol
Surface area48730 Å2
Unit cell
Length a, b, c (Å)231.676, 231.676, 168.955
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Transferrin receptor protein 1 / / TR / TfR / TfR1 / Trfr / T9 / p90 / Transferrin receptor protein 1 / serum form / sTfR


Mass: 73533.156 Da / Num. of mol.: 2 / Fragment: UNP residues 120-760
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TFR1, TFRC / Plasmid: pNUT / Production host: Cricetinae (hamsters) / Strain (production host): BHK cells / References: UniProt: P02786
#2: Protein Serotransferrin / Transferrin / Beta-1 metal-binding globulin / Siderophilin


Mass: 76980.367 Da / Num. of mol.: 2 / Fragment: UNP residues 20-698 / Mutation: N427D,Y440F, Y531F N625D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRO1400, TF / Plasmid: pNUT / Production host: Cricetinae (hamsters) / Strain (production host): BHK cells / References: UniProt: P02787

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Sugars , 1 types, 2 molecules

#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 6 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#6: Chemical ChemComp-CO3 / CARBONATE ION / Carbonate


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3

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Details

Sequence detailsI448V IS IS A NATURAL VARIANT, AS PER THE AUTHORS G142S IS ALSO A NATURAL VARIANT

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.77 Å3/Da / Density % sol: 67.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 5% PEG 3350, 0.2 M MgCl2, 10% 1,2-propanediol, pH Hepes 7.5, vapor diffusion, hanging drop, temperature 293K
PH range: Hepes 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 8, 2010 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.22→30 Å / Num. obs: 74056 / % possible obs: 100 % / Redundancy: 30.6 % / Rmerge(I) obs: 0.142 / Χ2: 1.351 / Net I/σ(I): 8.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.22-3.3320.70.99172671.164199.7
3.33-3.4726.60.78673001.3511100
3.47-3.63300.60873091.3041100
3.63-3.8230.90.42273401.4531100
3.82-4.0631.70.30173521.4411100
4.06-4.3732.80.19373451.3781100
4.37-4.8133.60.13474151.3591100
4.81-5.533.80.1274341.341100
5.5-6.9133.30.10874901.4141100
6.91-3031.90.0478041.24199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 44.08 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.22 Å29.94 Å
Translation3.22 Å29.94 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
CNSrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
RefinementResolution: 3.22→30 Å / Occupancy max: 1 / Occupancy min: 0.65 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.3143 7464 10 %
Rwork0.2714 66372 -
obs-73836 99.1 %
Solvent computationBsol: 71.0148 Å2
Displacement parametersBiso max: 200 Å2 / Biso mean: 114.8454 Å2 / Biso min: 16.99 Å2
Baniso -1Baniso -2Baniso -3
1-17.92 Å20 Å20 Å2
2--17.92 Å20 Å2
3----35.84 Å2
Refine analyzeLuzzati coordinate error obs: 0.59 Å
Refinement stepCycle: LAST / Resolution: 3.22→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16673 0 40 0 16713
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:carbohydrate.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION5co3.param

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