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- PDB-6y76: AP01 - a redesigned transferrin receptor apical domain -

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Basic information

Entry
Database: PDB / ID: 6y76
TitleAP01 - a redesigned transferrin receptor apical domain
ComponentsTransferrin receptor protein 1
KeywordsCYTOSOLIC PROTEIN / transferrin receptor / transferrin / protein design / Rosetta
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
Transferrin receptor protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsOberdorfer, G. / Berger, S.A. / Bjelic, S. / Sjostrom, D.J.
Funding support Austria, Sweden, 2items
OrganizationGrant numberCountry
Austrian Science FundP30826 Austria
Vinnova Sweden
CitationJournal: Proteins / Year: 2020
Title: Computational backbone design enables soluble engineering of transferrin receptor apical domain.
Authors: Sjostrom, D.J. / Berger, S.A. / Oberdorfer, G. / Bjelic, S.
History
DepositionFeb 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _struct_conn.pdbx_dist_value / _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_symmetry / _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_conn.ptnr2_symmetry
Revision 1.2Jan 13, 2021Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3May 1, 2024Group: 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
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1745
Polymers36,1052
Non-polymers693
Water3,675204
1
A: Transferrin receptor protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0752
Polymers18,0521
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transferrin receptor protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0983
Polymers18,0521
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.122, 119.558, 33.167
Angle α, β, γ (deg.)90.000, 112.249, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 or resid 3 through 31 or resid 33 through 52 or resid 54 through 156))
d_2ens_1(chain "B" and (resid 1 or resid 3 through 31 or resid 33 through 52 or resid 54 through 156))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1METMETA1
d_12ens_1ASNALAA4 - 32
d_13ens_1VALTYRA34 - 53
d_14ens_1PROSERA56 - 158
d_21ens_1METMETB1
d_22ens_1ASNALAB3 - 31
d_23ens_1VALTYRB34 - 53
d_24ens_1PROSERB55 - 157

NCS oper: (Code: givenMatrix: (-0.378204206956, 0.00160596258377, 0.925720799553), (0.00407113208187, -0.999985939421, 0.00339806482145), (0.925713240547, 0.00505389405689, 0.3781923511)Vector: 13. ...NCS oper: (Code: given
Matrix: (-0.378204206956, 0.00160596258377, 0.925720799553), (0.00407113208187, -0.999985939421, 0.00339806482145), (0.925713240547, 0.00505389405689, 0.3781923511)
Vector: 13.6649257392, 20.6271732556, -9.21138041029)

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Components

#1: Protein Transferrin receptor protein 1 / Trfr / T9 / p90


Mass: 18052.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TFRC / Production host: Escherichia coli (E. coli) / References: UniProt: P02786
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium fluoride and 20% v/v PEG 3350

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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 PILATUS 6M / Detector: PIXEL / Date: Mar 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.98→30.7 Å / Num. obs: 15946 / % possible obs: 96.61 % / Redundancy: 3.4 % / Biso Wilson estimate: 21.33 Å2 / CC1/2: 0.991 / Net I/σ(I): 7.61
Reflection shellResolution: 1.985→2.056 Å / Num. unique obs: 1375 / CC1/2: 0.875

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Processing

Software
NameVersionClassification
PHENIX1.18rc1_3777refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Design model

Resolution: 1.98→30.7 Å / SU ML: 0.2664 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 29.9405
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2745 1595 10.01 %
Rwork0.2344 14341 -
obs0.2384 15936 96.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.73 Å2
Refinement stepCycle: LAST / Resolution: 1.98→30.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2336 0 3 204 2543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00362394
X-RAY DIFFRACTIONf_angle_d0.82223242
X-RAY DIFFRACTIONf_chiral_restr0.0517387
X-RAY DIFFRACTIONf_plane_restr0.0048416
X-RAY DIFFRACTIONf_dihedral_angle_d16.1195879
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.51724899172 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.050.32031250.27921119X-RAY DIFFRACTION81.2
2.05-2.120.32391410.25781271X-RAY DIFFRACTION96.91
2.12-2.210.3041500.24151352X-RAY DIFFRACTION98.04
2.21-2.310.3511430.24291277X-RAY DIFFRACTION97.66
2.31-2.430.28721460.24161313X-RAY DIFFRACTION98.05
2.43-2.580.29331500.23521356X-RAY DIFFRACTION98.75
2.58-2.780.29291470.24091320X-RAY DIFFRACTION98.59
2.78-3.060.28891490.24811338X-RAY DIFFRACTION98.74
3.06-3.50.27071440.23131295X-RAY DIFFRACTION97.89
3.5-4.40.22961490.20961344X-RAY DIFFRACTION98.48
4.41-30.70.23691510.22911356X-RAY DIFFRACTION98.88

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