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- PDB-3kas: Machupo virus GP1 bound to human transferrin receptor 1 -

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Basic information

Entry
Database: PDB / ID: 3kas
TitleMachupo virus GP1 bound to human transferrin receptor 1
Components
  • Glycoprotein
  • Transferrin receptor protein 1
KeywordsVIRAL PROTEIN/ENDOCYTOSIS / Machupo virus / transferrin receptor 1 / arenavirus / Cell membrane / Disulfide bond / Endocytosis / Glycoprotein / Host-virus interaction / Receptor / Secreted / Transmembrane / VIRAL PROTEIN-ENDOCYTOSIS 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 iron ion / response to copper 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 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 / host cell Golgi membrane / RHOC GTPase cycle / RHOQ GTPase cycle / RHOH GTPase cycle / CDC42 GTPase cycle / transport across blood-brain barrier / 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 / Hsp70 protein binding / positive regulation of T cell proliferation / RAC1 GTPase cycle / cellular response to leukemia inhibitory factor / osteoclast differentiation / response to nutrient / acute-phase response / positive regulation of protein-containing complex assembly / clathrin-coated endocytic vesicle membrane / receptor internalization / HFE-transferrin receptor complex / recycling endosome / positive regulation of protein localization to nucleus / recycling endosome membrane / extracellular vesicle / melanosome / cellular response to xenobiotic stimulus / double-stranded RNA binding / Cargo recognition for clathrin-mediated endocytosis / virus receptor activity / Clathrin-mediated endocytosis / positive regulation of peptidyl-serine phosphorylation / positive regulation of NF-kappaB transcription factor activity / iron ion transport / cytoplasmic vesicle / basolateral plasma membrane / blood microparticle / positive regulation of canonical NF-kappaB signal transduction / intracellular iron ion homeostasis / receptor-mediated endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / response to hypoxia / early endosome / endosome membrane / endosome / intracellular signal transduction / positive regulation of protein phosphorylation / external side of plasma membrane / intracellular membrane-bounded organelle / fusion of virus membrane with host endosome membrane / viral envelope / protein-containing complex binding / virion attachment to host cell / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / host cell plasma membrane / virion membrane / perinuclear region of cytoplasm / cell surface / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome / extracellular region / membrane / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
Transferrin receptor protein 1/2, PA domain / Transferrin receptor-like, dimerisation domain / Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein / 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 ...Transferrin receptor protein 1/2, PA domain / Transferrin receptor-like, dimerisation domain / Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein / 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
: / PHOSPHATE ION / Transferrin receptor protein 1 / Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesHomo sapiens (human)
Machupo virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAbraham, J. / Corbett, K.D. / Harrison, S.C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structural basis for receptor recognition by New World hemorrhagic fever arenaviruses.
Authors: Abraham, J. / Corbett, K.D. / Farzan, M. / Choe, H. / Harrison, S.C.
History
DepositionOct 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 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: Glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,73015
Polymers90,4302
Non-polymers3,29913
Water4,504250
1
A: Transferrin receptor protein 1
B: Glycoprotein
hetero molecules

A: Transferrin receptor protein 1
B: Glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,45930
Polymers180,8614
Non-polymers6,59926
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)143.951, 170.228, 98.471
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-18-

HOH

21A-842-

HOH

31B-280-

HOH

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 71807.258 Da / Num. of mol.: 1 / Fragment: residues 121-760
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P02786
#2: Protein Glycoprotein /


Mass: 18623.051 Da / Num. of mol.: 1 / Fragment: residues 83-244
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Machupo virus / Strain: Carvallo / Plasmid: pFastBac1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8AZ57

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Sugars , 3 types, 6 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#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 / N-Acetylglucosamine


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, 257 molecules

#6: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 3.34 Å3/Da / Density % sol: 63.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.6 M sodium potassium phosphate, 150 mM NaCl, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2008 / Details: mirrors
RadiationMonochromator: side-bounce cryogenically-cooled 220 silicon monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 42215 / Num. obs: 42215 / % possible obs: 88.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Biso Wilson estimate: 48.24 Å2 / Rsym value: 0.099 / Net I/σ(I): 14.4
Reflection shellResolution: 2.4→2.47 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.767 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.767 / % possible all: 36.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.4_162)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CX8

1cx8


Resolution: 2.4→33.132 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.29 / σ(F): 1.35 / Phase error: 26.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2377 2084 4.94 %
Rwork0.1893 --
obs0.1917 42181 88.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.509 Å2 / ksol: 0.329 e/Å3
Displacement parametersBiso mean: 54.778 Å2
Baniso -1Baniso -2Baniso -3
1--0.953 Å2-0 Å20 Å2
2---2.833 Å2-0 Å2
3---3.786 Å2
Refinement stepCycle: LAST / Resolution: 2.4→33.132 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6259 0 208 250 6717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076628
X-RAY DIFFRACTIONf_angle_d1.0498990
X-RAY DIFFRACTIONf_dihedral_angle_d21.7262428
X-RAY DIFFRACTIONf_chiral_restr0.1641009
X-RAY DIFFRACTIONf_plane_restr0.0041124
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.45580.3408490.2719978X-RAY DIFFRACTION33
2.4558-2.51720.3507880.26741550X-RAY DIFFRACTION52
2.5172-2.58530.2997870.26642048X-RAY DIFFRACTION68
2.5853-2.66130.34981210.27372437X-RAY DIFFRACTION81
2.6613-2.74720.31511340.26052832X-RAY DIFFRACTION95
2.7472-2.84530.29831650.23962970X-RAY DIFFRACTION100
2.8453-2.95910.28261670.2272977X-RAY DIFFRACTION100
2.9591-3.09370.2611510.21843011X-RAY DIFFRACTION100
3.0937-3.25670.27371650.20912977X-RAY DIFFRACTION100
3.2567-3.46050.2111530.18433017X-RAY DIFFRACTION100
3.4605-3.72740.24481550.17633008X-RAY DIFFRACTION100
3.7274-4.10190.20841700.15493023X-RAY DIFFRACTION100
4.1019-4.6940.18081690.13343026X-RAY DIFFRACTION100
4.694-5.90850.19061640.14943054X-RAY DIFFRACTION100
5.9085-33.13470.23381460.18663189X-RAY DIFFRACTION100
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)
12.1924-0.12870.30441.19350.76011.05290.05370.14230.00140.0555-0.07960.01580.0613-0.00350.00910.15040.02730.03930.13550.04170.1436-56.614360.121619.5706
20.9330.2276-0.22471.2273-0.08660.6898-0.05650.0285-0.11310.10690.0590.0371-0.0742-0.0157-0.00180.13570.036-0.00590.1166-0.02810.1211-17.021718.017215.3102
31.342-0.99870.29850.87570.38080.61030.07850.21380.10190.00150.001-0.1182-0.03170.0713-0.06370.20810.06060.04770.2429-0.02860.2383-30.865546.602817.5496
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain BB86 - 241
2X-RAY DIFFRACTION2chain A and (resid 121:188 or resid 383:760 or resid 1011)A121 - 188
3X-RAY DIFFRACTION2chain A and (resid 121:188 or resid 383:760 or resid 1011)A383 - 760
4X-RAY DIFFRACTION2chain A and (resid 121:188 or resid 383:760 or resid 1011)A1011
5X-RAY DIFFRACTION3chain A and (resid 189:382 or resid 1001)A189 - 382
6X-RAY DIFFRACTION3chain A and (resid 189:382 or resid 1001)A1001

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