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- PDB-6okd: Crystal Structure of human transferrin receptor in complex with a... -

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Basic information

Entry
Database: PDB / ID: 6okd
TitleCrystal Structure of human transferrin receptor in complex with a cystine-dense peptide
Components
  • Transferrin receptor protein 1
  • transferrin receptor binding cystine-dense peptide
KeywordsTRANSPORT PROTEIN/SIGNALING PROTEIN / protein-protein complex / cystine-dense peptide / TRANSPORT PROTEIN-SIGNALING PROTEIN complex
Function / homology
Function and homology information


transferrin receptor activity / negative regulation of mitochondrial fusion / transferrin transport / Transferrin endocytosis and recycling / positive regulation of isotype switching / response to copper ion / response to iron ion / response to manganese ion / RND1 GTPase cycle / RND2 GTPase cycle ...transferrin receptor activity / negative regulation of mitochondrial fusion / transferrin transport / Transferrin endocytosis and recycling / positive regulation of isotype switching / response to copper ion / response to iron 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 / CDC42 GTPase cycle / RHOH GTPase cycle / transport across blood-brain barrier / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / positive regulation of bone resorption / response to retinoic acid / positive regulation of T cell proliferation / clathrin-coated pit / positive regulation of B cell proliferation / Hsp70 protein binding / RAC1 GTPase cycle / response to nutrient / osteoclast differentiation / cellular response to leukemia inhibitory factor / acute-phase response / clathrin-coated endocytic vesicle membrane / positive regulation of protein-containing complex assembly / HFE-transferrin receptor complex / receptor internalization / recycling endosome / positive regulation of protein localization to nucleus / 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 / virus receptor activity / positive regulation of NF-kappaB transcription factor activity / iron ion transport / cytoplasmic vesicle / basolateral plasma membrane / positive regulation of canonical NF-kappaB signal transduction / intracellular iron ion homeostasis / early endosome / blood microparticle / endosome membrane / response to hypoxia / 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 / 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 ...Transferrin receptor protein 1/2, PA domain / 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 / Glucose Oxidase; domain 1 / Peptidase M28 / Peptidase family M28 / Zn peptidases / Aminopeptidase / 3-Layer(bba) Sandwich / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Transferrin receptor protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Monosiga brevicollis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsFinton, K.A.K. / Rupert, P.B. / Strong, R.K.
CitationJournal: J.Mol.Biol. / Year: 2020
Title: A TfR-Binding Cystine-Dense Peptide Promotes Blood-Brain Barrier Penetration of Bioactive Molecules.
Authors: Crook, Z.R. / Girard, E. / Sevilla, G.P. / Merrill, M. / Friend, D. / Rupert, P.B. / Pakiam, F. / Nguyen, E. / Yin, C. / Ruff, R.O. / Hopping, G. / Strand, A.D. / Finton, K.A.K. / Coxon, M. ...Authors: Crook, Z.R. / Girard, E. / Sevilla, G.P. / Merrill, M. / Friend, D. / Rupert, P.B. / Pakiam, F. / Nguyen, E. / Yin, C. / Ruff, R.O. / Hopping, G. / Strand, A.D. / Finton, K.A.K. / Coxon, M. / Mhyre, A.J. / Strong, R.K. / Olson, J.M.
History
DepositionApr 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: transferrin receptor binding cystine-dense peptide
D: transferrin receptor binding cystine-dense peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,22120
Polymers162,0254
Non-polymers2,19616
Water14,088782
1
A: Transferrin receptor protein 1
D: transferrin receptor binding cystine-dense peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0189
Polymers81,0122
Non-polymers1,0067
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-5 kcal/mol
Surface area26680 Å2
MethodPISA
2
B: Transferrin receptor protein 1
C: transferrin receptor binding cystine-dense peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,20311
Polymers81,0122
Non-polymers1,1909
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-4 kcal/mol
Surface area26670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.601, 145.500, 133.494
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 4 molecules ABCD

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


Mass: 75052.688 Da / Num. of mol.: 2 / Fragment: ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TFRC / Plasmid: Daedalus system / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P02786
#2: Protein transferrin receptor binding cystine-dense peptide


Mass: 5959.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monosiga brevicollis (eukaryote) / Strain: randomly mutated / Gene: cytochrome BC1 complex subunit 6 / Plasmid: Daedalus system / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

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Sugars , 1 types, 4 molecules

#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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, 794 molecules

#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 782 / Source method: isolated from a natural source / Formula: H2O

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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: 3.36 Å3/Da / Density % sol: 63.35 % / Mosaicity: 0.346 ° / Mosaicity esd: 0.003 °
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5 / Details: PEG 6000, Mes

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 166017 / % possible obs: 99.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.056 / Rrim(I) all: 0.103 / Χ2: 1.156 / Net I/σ(I): 8.3 / Num. measured all: 551226
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.883.30.69381980.6640.4410.8240.47899.9
1.88-1.923.30.59883120.7220.3820.7120.51399.9
1.92-1.953.30.49582950.7870.3170.5890.527100
1.95-1.993.30.41482760.8220.2680.4940.558100
1.99-2.043.20.32682890.8570.2170.3930.58399.9
2.04-2.083.20.27883370.8890.1830.3340.62899.9
2.08-2.143.20.24383080.9210.1590.2910.643100
2.14-2.193.50.2182430.9440.1310.2470.677100
2.19-2.263.40.18283090.9540.1140.2150.78399.9
2.26-2.333.40.15683240.9650.0990.1850.81999.9
2.33-2.413.30.13882720.9690.0890.1650.88100
2.41-2.513.20.12283170.9740.0810.1471.03599.7
2.51-2.633.30.1183160.9790.0710.1311.14199.9
2.63-2.763.50.09782780.9850.0610.1151.24999.9
2.76-2.943.40.08582990.9880.0540.11.51399.9
2.94-3.163.30.07183030.9910.0460.0851.7999.7
3.16-3.483.30.05983280.9920.0390.0712.2499.7
3.48-3.993.50.05282810.9950.0330.0622.599.6
3.99-5.023.20.04383270.9960.0280.0512.38299.1
5.02-503.40.03884050.9980.0240.0452.09299.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.59 Å41.58 Å
Translation3.59 Å41.58 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0158refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.7.17phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 1de4

1de4


Resolution: 1.85→50.01 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.431 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18714 8375 5 %RANDOM
Rwork0.16278 ---
obs0.16405 157641 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.399 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å2-0.17 Å2
2--0.57 Å20 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.85→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10156 0 140 782 11078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01910575
X-RAY DIFFRACTIONr_bond_other_d0.0010.029557
X-RAY DIFFRACTIONr_angle_refined_deg1.6111.96114376
X-RAY DIFFRACTIONr_angle_other_deg0.85322105
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8451331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.6324.33455
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.644151651
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6431545
X-RAY DIFFRACTIONr_chiral_restr0.1990.21637
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.0211781
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022208
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1871.7895294
X-RAY DIFFRACTIONr_mcbond_other2.1871.7895293
X-RAY DIFFRACTIONr_mcangle_it2.8422.9926602
X-RAY DIFFRACTIONr_mcangle_other2.8422.9926603
X-RAY DIFFRACTIONr_scbond_it3.9292.3345281
X-RAY DIFFRACTIONr_scbond_other3.9292.3355282
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4733.6967764
X-RAY DIFFRACTIONr_long_range_B_refined6.64117.8412022
X-RAY DIFFRACTIONr_long_range_B_other6.64217.84212023
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.848→1.896 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 519 -
Rwork0.229 11163 -
obs--95.01 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.86151.1281-0.26670.8297-0.01210.55840.0238-0.2045-0.03010.0562-0.1004-0.03490.0065-0.02520.07660.0059-0.0039-0.00350.019-0.00310.0143127.55296.733452.7398
21.0392-0.53590.04711.27330.25651.47890.10290.13990.0419-0.1941-0.1694-0.02070.0202-0.01650.06650.03350.0280.01350.02840.00720.0439112.81380.204635.1667
33.0692-1.23980.15080.87750.01270.53470.0260.2028-0.006-0.059-0.0987-0.0059-0.0087-0.04210.07270.00650.00390.0010.0188-0.00710.0111123.5127-42.661814.4691
41.06330.668-0.11.45460.35641.45870.1195-0.1776-0.0480.2412-0.1871-0.0484-0.01090.02030.06760.0446-0.0354-0.01860.03850.02150.0508114.4762-37.030734.3538
513.06295.84332.7842.62461.26374.66290.0226-0.16940.40740.0041-0.07460.23970.1461-0.41190.05210.2734-0.05010.00180.2161-0.03340.3342101.5728-39.707251.3178
612.52523.2634.42122.36081.01474.16790.1479-0.69030.48020.4124-0.2585-0.0133-0.0627-0.08910.11060.3059-0.1147-0.01460.31910.01690.1352112.8174-36.638160.0806
78.3443-1.76832.1243.196-1.72421.1241-0.1958-0.32030.17780.23580.0634-0.1266-0.1697-0.02860.13230.5681-0.1088-0.0330.49350.0410.4117122.8506-34.596966.0487
89.14642.21556.01232.35182.72788.5280.0185-0.40910.01910.2592-0.1595-0.1161-0.05810.07980.1410.182-0.0869-0.01730.18120.09280.1324112.4121-44.224852.4092
98.957-0.3425-5.2355.7717-1.54039.72930.20140.41230.028-0.3022-0.2320.2359-0.0867-0.26710.03060.21660.093-0.03920.219-0.00850.0997105.93771.564412.0861
1012.261-3.60156.315110.82482.847711.82640.19580.1278-0.2963-0.4481-0.25650.0160.2232-0.12750.06070.30380.12930.04630.32910.01290.1336116.4848-2.04215.2683
113.8173-5.67260.02358.4467-0.04160.0250.15280.030.0646-0.3321-0.075-0.13320.0781-0.0521-0.07780.521-0.010.02370.54130.0290.5045123.3923-1.95951.6327
129.3413-2.4024-6.53661.97062.47269.02240.04190.39550.0474-0.2521-0.1593-0.08940.01320.05240.11740.17870.08390.030.16780.07690.1226112.02427.42914.6975
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 280
2X-RAY DIFFRACTION2A281 - 637
3X-RAY DIFFRACTION3B3 - 337
4X-RAY DIFFRACTION4B338 - 637
5X-RAY DIFFRACTION5C3 - 9
6X-RAY DIFFRACTION6C10 - 21
7X-RAY DIFFRACTION7C22 - 33
8X-RAY DIFFRACTION8C34 - 51
9X-RAY DIFFRACTION9D4 - 14
10X-RAY DIFFRACTION10D15 - 22
11X-RAY DIFFRACTION11D23 - 34
12X-RAY DIFFRACTION12D35 - 51

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