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- PDB-6eah: CRYSTAL STRUCTURE OF HUMAN RESPIRATORY SYNCYTIAL VIRUS FUSION GLY... -

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Basic information

Entry
Database: PDB / ID: 6eah
TitleCRYSTAL STRUCTURE OF HUMAN RESPIRATORY SYNCYTIAL VIRUS FUSION GLYCOPROTEIN INHIBITOR ESCAPE VARIANT K394R-S398L STABILIZED IN THE PREFUSION STATE
ComponentsFusion glycoprotein F0
KeywordsVIRAL PROTEIN / CLASS I VIRAL FUSION PROTEIN / FUSION / RESPIRATORY SYNCYTIAL VIRUS / PREFUSION / FUSION INHIBITOR
Function / homology
Function and homology information


positive regulation of syncytium formation by virus / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane ...positive regulation of syncytium formation by virus / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / identical protein binding / plasma membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0
Similarity search - Domain/homology
Fusion glycoprotein F0 / Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respiratory syncytial virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBattles, M.B. / McLellan, J.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5T32AI007519-18 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM113132 United States
CitationJournal: To be published
Title: Structural Basis for Respiratory Syncytial Virus Fusion Inhibitor Resistance
Authors: Battles, M.B. / McLellan, J.S.
History
DepositionAug 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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_validate_close_contact / struct_asym / struct_conn / 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 / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fusion glycoprotein F0
B: Fusion glycoprotein F0
C: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,51625
Polymers189,8173
Non-polymers2,69922
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18780 Å2
ΔGint-293 kcal/mol
Surface area49460 Å2
Unit cell
Length a, b, c (Å)166.639, 166.639, 174.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 26 through 64 or resid 73...
21(chain B and (resid 26 through 64 or resid 73 through 207 or resid 214 through 506))
31(chain C and (resid 26 through 103 or resid 137 through 207 or resid 214 through 506))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNILEILE(chain A and (resid 26 through 64 or resid 73...AA26 - 6426 - 64
12ASPASPTHRTHR(chain A and (resid 26 through 64 or resid 73...AA73 - 10373 - 103
13PHEPHELEULEU(chain A and (resid 26 through 64 or resid 73...AA137 - 207137 - 207
14ILEILEILEILE(chain A and (resid 26 through 64 or resid 73...AA214 - 506214 - 506
21GLNGLNILEILE(chain B and (resid 26 through 64 or resid 73 through 207 or resid 214 through 506))BB26 - 6426 - 64
22ASPASPLEULEU(chain B and (resid 26 through 64 or resid 73 through 207 or resid 214 through 506))BB73 - 20773 - 207
23ILEILEILEILE(chain B and (resid 26 through 64 or resid 73 through 207 or resid 214 through 506))BB214 - 506214 - 506
31GLNGLNTHRTHR(chain C and (resid 26 through 103 or resid 137 through 207 or resid 214 through 506))CC26 - 10326 - 103
32PHEPHELEULEU(chain C and (resid 26 through 103 or resid 137 through 207 or resid 214 through 506))CC137 - 207137 - 207
33ILEILEILEILE(chain C and (resid 26 through 103 or resid 137 through 207 or resid 214 through 506))CC214 - 506214 - 506

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Components

#1: Protein Fusion glycoprotein F0


Mass: 63272.438 Da / Num. of mol.: 3 / Fragment: RSV F ectodomain / Mutation: S155C, S290C, S190F, V207L, K394R, S398L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus / Plasmid: P(ALPHA)H / Production host: Homo sapiens (human) / Strain (production host): HEK293 FREESTYLE / References: UniProt: W8RJF9, UniProt: P03420*PLUS
#2: 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
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM

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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: 3.18 Å3/Da / Density % sol: 61.37 % / Mosaicity: 0.3 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 1.48M K/Na tartrate, 0.2M LiSO4, 0.1M CHES pH 9.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 15, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→60.2 Å / Num. obs: 49640 / % possible obs: 99.9 % / Redundancy: 8.5 % / Biso Wilson estimate: 71.9 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.054 / Rrim(I) all: 0.162 / Net I/σ(I): 8.4 / Num. measured all: 423443 / Scaling rejects: 2663
Reflection shellResolution: 3→3.1 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.866 / Num. unique obs: 4475 / CC1/2: 0.625 / Rpim(I) all: 0.341 / Rrim(I) all: 0.934 / % possible all: 99.3

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Processing

Software
NameVersionClassification
Aimless0.5.26data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EA4

5ea4


Resolution: 3→58.916 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.17
RfactorNum. reflection% reflection
Rfree0.2186 2439 4.92 %
Rwork0.1929 --
obs0.1943 49575 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 203.4 Å2 / Biso mean: 84.2811 Å2 / Biso min: 27.36 Å2
Refinement stepCycle: final / Resolution: 3→58.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10256 0 151 0 10407
Biso mean--132.25 --
Num. residues----1325
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3897X-RAY DIFFRACTION3.484TORSIONAL
12B3897X-RAY DIFFRACTION3.484TORSIONAL
13C3897X-RAY DIFFRACTION3.484TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.06130.3441270.31652710283799
3.0613-3.12780.26891300.284427442874100
3.1278-3.20060.29691320.264727192851100
3.2006-3.28060.26331310.241927482879100
3.2806-3.36930.2621470.228827452892100
3.3693-3.46840.22361400.212227332873100
3.4684-3.58040.22221490.200127422891100
3.5804-3.70830.21261420.195527602902100
3.7083-3.85680.2531380.190727372875100
3.8568-4.03230.1881380.186927672905100
4.0323-4.24480.18811540.165227482902100
4.2448-4.51070.1641370.153927822919100
4.5107-4.85880.18391550.146127542909100
4.8588-5.34740.21251560.168328032959100
5.3474-6.12050.22761650.192727882953100
6.1205-7.70850.21321590.204128443003100
7.7085-58.92710.23211390.193730123151100
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)
11.0351-0.39190.24111.9045-1.032.55890.03410.30040.3204-0.1790.1117-0.3397-0.53050.1271-0.12880.4623-0.10950.10090.48230.05590.5147-45.147710.5155-13.6161
23.28182.0981-2.881.215-1.6925.6992-0.42860.5328-0.0128-1.29230.3413-0.9110.6462-0.55590.2950.7691-0.01080.2170.6348-0.01040.5681-61.04415.4167-8.2117
33.04431.1462-2.23922.0052-2.15167.5114-0.13940.42790.4847-0.10610.0136-0.2352-1.8366-0.1954-0.00731.2111-0.11860.24950.44830.20340.8375-47.54229.2865-20.1916
41.72880.7924-0.91971.3624-3.05138.5164-0.34240.25130.3482-0.4685-0.0886-0.6196-0.01790.50430.33390.7194-0.00320.20110.39790.12940.6624-44.295515.657-11.6634
52.3939-0.39870.35626.24231.19483.02870.0389-0.1848-0.15580.27580.02360.05530.0804-0.005-0.04660.22560.0082-0.04010.34480.01390.228-51.6173-10.07411.6693
65.1468-1.7141-2.72325.19140.42294.9512-0.04510.1602-0.72570.0444-0.0782-0.3060.36860.12110.08270.28450.0415-0.08050.31280.08950.3327-39.8946-23.99886.5554
78.7561-0.3488-2.80963.2975-0.81144.0237-0.0176-0.459-0.45270.2005-0.0330.07290.3065-0.13450.06110.4323-0.0088-0.05810.29310.06110.286-47.4743-23.353712.8176
81.57881.9664-0.44023.01650.17180.86740.14330.14360.5316-0.0710.03050.0928-0.20180.2557-0.19120.34120.06420.0410.48820.09520.7846-35.1507-5.8456-13.0405
93.06282.257-0.46813.00540.27740.9901-0.07240.58680.491-0.28770.2631-0.3879-0.16490.4259-0.14090.3578-0.02270.02520.59560.22010.7209-30.3984-8.0666-13.9372
103.48310.03521.07191.9256-0.34722.96270.0841-0.0178-0.27880.0735-0.089-0.00230.4227-0.06010.02550.3629-0.00140.00990.2393-0.02530.3689-60.1567-30.4032-15.1907
118.43-0.5713-7.05491.47270.74675.73150.11820.16260.2861-0.1436-0.25990.2513-0.6448-0.21010.00210.45520.0494-0.03170.38390.03150.3824-76.6405-0.4906-11.6242
126.06874.0347-2.11174.2793-0.26342.7922-0.0462-0.1165-0.4996-0.245-0.1253-0.8647-0.06610.54380.22240.5938-0.11540.22440.91020.12820.6832-33.2423-1.9683-36.0391
136.28122.3734-2.6863.6849-2.74361.8638-0.1825-0.3563-1.2034-0.1629-0.4806-0.9199-0.59111.02180.45670.4868-0.09620.01970.5272-0.020.6-52.6302-16.9125-24.4951
146.53522.5125-1.38353.6787-0.58531.00330.45071.22820.1715-1.3022-0.2933-0.2705-0.82790.6067-0.08750.9504-0.23080.37351.29490.17340.4729-39.9963-2.2317-46.626
155.77881.1945-2.04082.1778-0.98330.68670.62-0.00920.7992-0.1055-0.4482-0.277-0.62260.3794-0.12030.5972-0.16120.18210.6970.01130.4684-48.60040.4638-33.3531
162.41160.2095-1.4362.345-0.17279.0319-0.0955-0.06070.0670.02780.01340.0128-0.18210.22110.10290.27380.0238-0.04590.272-0.02660.3409-71.9524-7.9421-10.1498
172.67162.07150.40787.03040.63281.8868-0.0863-0.0042-0.12540.14230.03070.10560.1214-0.28770.0660.31440.02360.07160.40140.01570.2323-74.5412-5.08943.171
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 97 )A26 - 97
2X-RAY DIFFRACTION2chain 'A' and (resid 98 through 158 )A98 - 158
3X-RAY DIFFRACTION3chain 'A' and (resid 159 through 216 )A159 - 216
4X-RAY DIFFRACTION4chain 'A' and (resid 217 through 309 )A217 - 309
5X-RAY DIFFRACTION5chain 'A' and (resid 310 through 394 )A310 - 394
6X-RAY DIFFRACTION6chain 'A' and (resid 395 through 430 )A395 - 430
7X-RAY DIFFRACTION7chain 'A' and (resid 431 through 506 )A431 - 506
8X-RAY DIFFRACTION8chain 'B' and (resid 26 through 148 )B26 - 148
9X-RAY DIFFRACTION9chain 'B' and (resid 149 through 352 )B149 - 352
10X-RAY DIFFRACTION10chain 'B' and (resid 353 through 506 )B353 - 506
11X-RAY DIFFRACTION11chain 'C' and (resid 26 through 49 )C26 - 49
12X-RAY DIFFRACTION12chain 'C' and (resid 50 through 97 )C50 - 97
13X-RAY DIFFRACTION13chain 'C' and (resid 98 through 158 )C98 - 158
14X-RAY DIFFRACTION14chain 'C' and (resid 159 through 216 )C159 - 216
15X-RAY DIFFRACTION15chain 'C' and (resid 217 through 309 )C217 - 309
16X-RAY DIFFRACTION16chain 'C' and (resid 310 through 383 )C310 - 383
17X-RAY DIFFRACTION17chain 'C' and (resid 384 through 506 )C384 - 506

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