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- PDB-9gh7: Complex of human TfR1 with a potent bicyclic peptide -

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Basic information

Entry
Database: PDB / ID: 9gh7
TitleComplex of human TfR1 with a potent bicyclic peptide
Components
  • Bicyclic peptide
  • Transferrin receptor protein 1
KeywordsTRANSPORT PROTEIN / Transferrin receptor protein 1
Function / homology
Function and homology information


transferrin receptor activity / postsynaptic recycling endosome membrane / negative regulation of mitochondrial fusion / positive regulation of isotype switching / Transferrin endocytosis and recycling / response to manganese ion / response to copper ion / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / response to iron ion / RND1 GTPase cycle ...transferrin receptor activity / postsynaptic recycling endosome membrane / negative regulation of mitochondrial fusion / positive regulation of isotype switching / Transferrin endocytosis and recycling / response to manganese ion / response to copper ion / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / response to iron ion / RND1 GTPase cycle / RND2 GTPase cycle / RHOB GTPase cycle / Golgi Associated Vesicle Biogenesis / RHOC GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / RHOH GTPase cycle / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / response to retinoic acid / regulation of postsynaptic membrane neurotransmitter receptor levels / transport across blood-brain barrier / clathrin-coated pit / positive regulation of B cell proliferation / positive regulation of T cell proliferation / RAC1 GTPase cycle / response to nutrient / Hsp70 protein binding / osteoclast differentiation / cellular response to leukemia inhibitory factor / transferrin transport / acute-phase response / positive regulation of protein-containing complex assembly / clathrin-coated endocytic vesicle membrane / iron ion transport / HFE-transferrin receptor complex / recycling endosome / receptor internalization / multicellular organismal-level iron ion homeostasis / positive regulation of protein localization to nucleus / recycling endosome membrane / Cargo recognition for clathrin-mediated endocytosis / cellular response to xenobiotic stimulus / Clathrin-mediated endocytosis / melanosome / extracellular vesicle / double-stranded RNA binding / virus receptor activity / cytoplasmic vesicle / blood microparticle / basolateral plasma membrane / intracellular iron ion homeostasis / response to hypoxia / early endosome / positive regulation of canonical NF-kappaB signal transduction / endosome membrane / endosome / intracellular signal transduction / external side of plasma membrane / intracellular membrane-bounded organelle / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / protein-containing complex binding / perinuclear region of cytoplasm / glutamatergic synapse / cell surface / protein homodimerization activity / extracellular space / RNA binding / 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
: / Transferrin receptor protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.079 Å
AuthorsPellegrino, S. / Pernigo, S. / Swan, M.K. / Bezerra, G.A. / Chen, L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Not funded United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Conjugation to a transferrin receptor 1-binding Bicycle peptide enhances ASO and siRNA potency in skeletal and cardiac muscles.
Authors: Ostergaard, M.E. / Carrer, M. / Anderson, B.A. / Afetian, M. / Bakooshli, M.A. / Santos, J.A. / Klein, S.K. / Capitanio, J. / Freestone, G.C. / Tanowitz, M. / Galindo-Murillo, R. / Gaus, H.J. ...Authors: Ostergaard, M.E. / Carrer, M. / Anderson, B.A. / Afetian, M. / Bakooshli, M.A. / Santos, J.A. / Klein, S.K. / Capitanio, J. / Freestone, G.C. / Tanowitz, M. / Galindo-Murillo, R. / Gaus, H.J. / Dwyer, C.A. / Jackson, M. / Jafar-Nejad, P. / Rigo, F. / Seth, P.P. / Gaynor, K.U. / Stanway, S.J. / Urbonas, L. / St Denis, M.A. / Pellegrino, S. / Bezerra, G.A. / Rigby, M. / Gowans, E. / Van Rietschoten, K. / Beswick, P. / Chen, L. / Skynner, M.J. / Swayze, E.E.
History
DepositionAug 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transferrin receptor protein 1
P: Bicyclic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8217
Polymers77,6272
Non-polymers1,1945
Water2,054114
1
A: Transferrin receptor protein 1
P: Bicyclic peptide
hetero molecules

A: Transferrin receptor protein 1
P: Bicyclic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,64214
Polymers155,2534
Non-polymers2,38810
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area11180 Å2
ΔGint-49 kcal/mol
Surface area46450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.955, 94.955, 225.997
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein / Protein/peptide / Sugars , 3 types, 4 molecules AP

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


Mass: 76081.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TFRC / Production host: Homo sapiens (human) / Strain (production host): Expi293f / References: UniProt: P02786
#2: Protein/peptide Bicyclic peptide


Mass: 1544.796 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Bicyclic peptide inhibitor. / Source: (synth.) synthetic construct (others)
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 117 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-A1ILE / 1-(3,5-diethanoyl-1,3,5-triazinan-1-yl)ethanone


Mass: 213.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N3O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 64.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M ammonium tartrate dibasic pH 7.0, 12% (w/v) PEG 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 15, 2021 / Details: 80x20
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.079→87.542 Å / Num. obs: 48208 / % possible obs: 95.7 % / Redundancy: 24.8 % / CC1/2: 1 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.016 / Rrim(I) all: 0.08 / Net I/σ(I): 23.1
Reflection shellResolution: 2.079→2.264 Å / Rmerge(I) obs: 1.256 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2411 / CC1/2: 0.769 / Rpim(I) all: 0.363 / Rrim(I) all: 1.308 / % possible all: 75.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.079→87.542 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.199 / SU B: 5.546 / SU ML: 0.138 / Average fsc free: 0.954 / Average fsc work: 0.9674 / Cross valid method: FREE R-VALUE / ESU R: 0.213 / ESU R Free: 0.185
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2351 2438 5.057 %Random selection
Rwork0.1983 45770 --
all0.2 ---
obs-48208 76.422 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 52.518 Å2
Baniso -1Baniso -2Baniso -3
1--0.079 Å20 Å20 Å2
2---0.079 Å20 Å2
3---0.158 Å2
Refinement stepCycle: LAST / Resolution: 2.079→87.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5098 0 78 114 5290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125308
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164935
X-RAY DIFFRACTIONr_angle_refined_deg1.7221.8097211
X-RAY DIFFRACTIONr_angle_other_deg0.5961.74811356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3225648
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.4725.55627
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.93810850
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg2.117103
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.5210238
X-RAY DIFFRACTIONr_chiral_restr0.0830.2807
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026226
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021242
X-RAY DIFFRACTIONr_nbd_refined0.2250.21179
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.24747
X-RAY DIFFRACTIONr_nbtor_refined0.1910.22711
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0950.22880
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2195
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0670.21
X-RAY DIFFRACTIONr_metal_ion_refined0.140.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1540.226
X-RAY DIFFRACTIONr_nbd_other0.1670.2144
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1810.213
X-RAY DIFFRACTIONr_mcbond_it4.265.1832599
X-RAY DIFFRACTIONr_mcbond_other4.265.1832599
X-RAY DIFFRACTIONr_mcangle_it5.839.3023244
X-RAY DIFFRACTIONr_mcangle_other5.8299.3023245
X-RAY DIFFRACTIONr_scbond_it5.245.6422709
X-RAY DIFFRACTIONr_scbond_other5.2395.6422710
X-RAY DIFFRACTIONr_scangle_it7.53710.1683967
X-RAY DIFFRACTIONr_scangle_other7.53610.1673968
X-RAY DIFFRACTIONr_lrange_it8.93151.9086055
X-RAY DIFFRACTIONr_lrange_other8.93151.9076056
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.079-2.1330.298130.3372560.33545730.9180.9135.88240.332
2.133-2.1910.362370.3167150.31844770.9350.93116.7970.305
2.191-2.2550.28560.28710950.28643480.9490.94326.47190.273
2.255-2.3240.312990.27917610.28142330.9390.94743.94050.256
2.324-2.40.3091320.27327930.27541010.9440.95271.32410.249
2.4-2.4840.322040.26236860.26539850.9390.95697.61610.236
2.484-2.5780.2851950.25736470.25838440.9510.9699.9480.224
2.578-2.6830.2972030.24534930.24836960.9460.9651000.212
2.683-2.8020.311670.23333850.23735520.9380.9681000.2
2.802-2.9390.2741730.22432250.22733990.9470.96999.97060.198
2.939-3.0980.2811560.2231080.22232640.9480.9711000.197
3.098-3.2850.271550.23329380.23530930.9510.9661000.217
3.285-3.5120.2831490.22827680.23129170.9540.9691000.217
3.512-3.7930.2621420.21225820.21427240.9630.9761000.207
3.793-4.1540.1981200.17424010.17525210.9780.9841000.179
4.154-4.6430.181300.14821600.1522900.980.9871000.167
4.643-5.3590.166990.15219540.15320530.9830.9861000.177
5.359-6.5570.278910.17516580.18117490.9640.9841000.201
6.557-9.2470.166720.15113340.15214060.9840.9891000.19
9.247-87.5420.146450.1818110.188560.9870.9721000.259

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