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- PDB-5f1b: Structural basis of Ebola virus entry: viral glycoprotein bound t... -

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Basic information

Entry
Database: PDB / ID: 5f1b
TitleStructural basis of Ebola virus entry: viral glycoprotein bound to its endosomal receptor Niemann-Pick C1
Components
  • GP1
  • GP2
  • Niemann-Pick C1 protein
KeywordsVIRAL PROTEIN/TRANSPORT PROTEIN / Ebola virus / glycoprotein / NPC1-C / VIRAL PROTEIN-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


cyclodextrin metabolic process / cholesterol storage / membrane raft organization / intracellular cholesterol transport / intracellular lipid transport / sterol transport / intestinal cholesterol absorption / LDL clearance / negative regulation of epithelial cell apoptotic process / bile acid metabolic process ...cyclodextrin metabolic process / cholesterol storage / membrane raft organization / intracellular cholesterol transport / intracellular lipid transport / sterol transport / intestinal cholesterol absorption / LDL clearance / negative regulation of epithelial cell apoptotic process / bile acid metabolic process / programmed cell death / cholesterol transfer activity / cholesterol transport / establishment of protein localization to membrane / adult walking behavior / cholesterol efflux / lysosomal transport / cholesterol binding / negative regulation of macroautophagy / cellular response to steroid hormone stimulus / protein glycosylation / cellular response to low-density lipoprotein particle stimulus / response to cadmium ion / negative regulation of TORC1 signaling / neurogenesis / cholesterol metabolic process / cholesterol homeostasis / liver development / macroautophagy / autophagy / endocytosis / late endosome membrane / transmembrane signaling receptor activity / nuclear envelope / signaling receptor activity / virus receptor activity / gene expression / clathrin-dependent endocytosis of virus by host cell / symbiont-mediated-mediated suppression of host tetherin activity / entry receptor-mediated virion attachment to host cell / lysosome / symbiont-mediated suppression of host innate immune response / membrane raft / response to xenobiotic stimulus / symbiont entry into host cell / lysosomal membrane / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / perinuclear region of cytoplasm / host cell plasma membrane / virion membrane / endoplasmic reticulum / Golgi apparatus / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
NPC1-like / Niemann-Pick C1, N-terminal / : / Niemann-Pick C1 N terminus / NPC1, middle luminal domain / : / Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / Envelope glycoprotein GP2-like, HR1-HR2 ...NPC1-like / Niemann-Pick C1, N-terminal / : / Niemann-Pick C1 N terminus / NPC1, middle luminal domain / : / Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / Envelope glycoprotein GP2-like, HR1-HR2 / : / Sterol-sensing domain of SREBP cleavage-activation / Sterol-sensing domain (SSD) profile. / Sterol-sensing domain
Similarity search - Domain/homology
NPC intracellular cholesterol transporter 1 / Envelope glycoprotein
Similarity search - Component
Biological speciesZaire ebolavirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWang, H. / Shi, Y. / Song, J. / Qi, J. / Lu, G. / Yan, J. / Gao, G.F.
Funding support China, 1items
OrganizationGrant numberCountry
China Ministry of Science and Technology National 973 Project2013CB531502 and 2014CB542503 China
CitationJournal: Cell / Year: 2016
Title: Ebola Viral Glycoprotein Bound to Its Endosomal Receptor Niemann-Pick C1.
Authors: Wang, H. / Shi, Y. / Song, J. / Qi, J. / Lu, G. / Yan, J. / Gao, G.F.
History
DepositionNov 30, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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_oper_list / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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
Revision 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GP1
B: GP2
C: Niemann-Pick C1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9384
Polymers61,5143
Non-polymers4241
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-24 kcal/mol
Surface area23250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.261, 107.261, 93.777
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein GP1 / GP1 / 2 / GP


Mass: 17194.543 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 32-188
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus / Strain: Kikwit-95 / Gene: GP / Cell line (production host): High Five cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P87666
#2: Protein GP2 / GP1 / 2 / GP


Mass: 14882.807 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 509-598
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus / Strain: Kikwit-95 / Gene: GP / Cell line (production host): High Five cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P87666
#3: Protein Niemann-Pick C1 protein


Mass: 29436.582 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 374-620
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NPC1 / Production host: Escherichia coli (E. coli) / References: UniProt: O15118
#4: 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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 15% (v/v) pentaerythritolpropoxylate, 0.2M sodium chloride, pH 5.5, 0.1M MES-NaOH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 27329 / % possible obs: 100 % / Redundancy: 19.6 % / Net I/σ(I): 32.6

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CSY

3csy


Resolution: 2.3→41.858 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2301 1369 5.01 %
Rwork0.1813 --
obs0.1837 27310 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→41.858 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3657 0 0 171 3828
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083761
X-RAY DIFFRACTIONf_angle_d1.1525123
X-RAY DIFFRACTIONf_dihedral_angle_d14.5711333
X-RAY DIFFRACTIONf_chiral_restr0.052567
X-RAY DIFFRACTIONf_plane_restr0.006667
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2992-2.38130.281410.23432557X-RAY DIFFRACTION100
2.3813-2.47670.28491270.2132567X-RAY DIFFRACTION100
2.4767-2.58940.25131460.20612584X-RAY DIFFRACTION100
2.5894-2.72590.26771370.20712594X-RAY DIFFRACTION100
2.7259-2.89660.27191420.19782586X-RAY DIFFRACTION100
2.8966-3.12020.28751090.20222603X-RAY DIFFRACTION100
3.1202-3.4340.25631440.19712601X-RAY DIFFRACTION100
3.434-3.93060.19761450.17132587X-RAY DIFFRACTION100
3.9306-4.95090.19041370.14672605X-RAY DIFFRACTION100
4.9509-41.86510.22221410.17482657X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 30.2833 Å / Origin y: -16.3893 Å / Origin z: -320.9409 Å
111213212223313233
T0.2617 Å20.0041 Å20.0421 Å2-0.2557 Å20.0374 Å2--0.2749 Å2
L0.358 °2-0.1253 °20.2223 °2-0.2324 °2-0.1891 °2--0.1052 °2
S-0.0216 Å °-0.0146 Å °0.0127 Å °-0.0221 Å °0.0372 Å °0.0583 Å °0.0118 Å °-0.0441 Å °-0 Å °
Refinement TLS groupSelection details: all

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