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- PDB-6oe4: Prefusion RSV F monomer bound by neutralizing antibody CR9501 -

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Basic information

Entry
Database: PDB / ID: 6oe4
TitlePrefusion RSV F monomer bound by neutralizing antibody CR9501
Components
  • CR9501 Fab Heavy Chain
  • CR9501 Fab Light Chain
  • Fusion glycoprotein F0
KeywordsViral protein/immune system / class I fusion protein / immunoglobulin / respiratory syncytial virus / trimerization / VIRAL PROTEIN / Viral protein-immune system complex
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respiratory syncytial virus A
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsMcLellan, J.S. / Gilman, M.S.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008704 United States
CitationJournal: Nat Commun / Year: 2019
Title: Transient opening of trimeric prefusion RSV F proteins.
Authors: Gilman, M.S.A. / Furmanova-Hollenstein, P. / Pascual, G. / B van 't Wout, A. / Langedijk, J.P.M. / McLellan, J.S.
History
DepositionMar 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fusion glycoprotein F0
D: Fusion glycoprotein F0
C: CR9501 Fab Light Chain
B: CR9501 Fab Heavy Chain
E: CR9501 Fab Heavy Chain
F: CR9501 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,04611
Polymers211,7366
Non-polymers3105
Water00
1
A: Fusion glycoprotein F0
C: CR9501 Fab Light Chain
B: CR9501 Fab Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,9925
Polymers105,8683
Non-polymers1242
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6220 Å2
ΔGint-26 kcal/mol
Surface area38350 Å2
MethodPISA
2
D: Fusion glycoprotein F0
E: CR9501 Fab Heavy Chain
F: CR9501 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,0546
Polymers105,8683
Non-polymers1863
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-25 kcal/mol
Surface area38700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.628, 153.389, 155.529
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain D and (resid 27 through 208 or resid 211 through 506))
12chain C
22chain F
13chain B
23chain E

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA27 - 506
211(chain D and (resid 27 through 208 or resid 211 through 506))D27 - 208
221(chain D and (resid 27 through 208 or resid 211 through 506))D211 - 506
112chain CC1 - 212
212chain FF1 - 212
113chain BB2 - 214
213chain EE2 - 214

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Fusion glycoprotein F0 / Protein F / Prefusion RSV F


Mass: 57943.457 Da / Num. of mol.: 2 / Mutation: S155C, S290C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A (strain A2)
Strain: A2 / Production host: Homo sapiens (human) / References: UniProt: P03420
#2: Antibody CR9501 Fab Light Chain


Mass: 23557.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody CR9501 Fab Heavy Chain


Mass: 24367.268 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2

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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: 3.06 Å3/Da / Density % sol: 59.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 4.2mg/mL monomeric prefusion F (DS-Cav1) + CR9501 Fab, 14.3% (w/v) PEG8000, 2.4% (v/v) 2-methyl-2,4-pentanediol (MPD), 0.1 M sodium citrate pH 5.5, 0.1 M sodium malonate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.3→53 Å / Num. obs: 38582 / % possible obs: 99.7 % / Redundancy: 6.1 % / Biso Wilson estimate: 60.94 Å2 / CC1/2: 0.963 / Rmerge(I) obs: 0.394 / Rpim(I) all: 0.173 / Rrim(I) all: 0.431 / Net I/σ(I): 5.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.3-3.456.51.75746280.5390.7611.91899.7
11.43-52.815.10.07610290.9950.0360.08598.1

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
Aimless0.5.28data scaling
PDB_EXTRACT3.24data extraction
iMOSFLM7.2.1data reduction
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→52.814 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.09
RfactorNum. reflection% reflection
Rfree0.2593 1819 4.73 %
Rwork0.2118 --
obs0.2139 38479 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 196.75 Å2 / Biso mean: 60.8061 Å2 / Biso min: 23.37 Å2
Refinement stepCycle: final / Resolution: 3.3→52.814 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13290 0 20 0 13310
Biso mean--47.93 --
Num. residues----1732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413584
X-RAY DIFFRACTIONf_angle_d0.8718478
X-RAY DIFFRACTIONf_chiral_restr0.0532172
X-RAY DIFFRACTIONf_plane_restr0.0052324
X-RAY DIFFRACTIONf_dihedral_angle_d11.9018247
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4008X-RAY DIFFRACTION6.069TORSIONAL
12D4008X-RAY DIFFRACTION6.069TORSIONAL
21C2013X-RAY DIFFRACTION6.069TORSIONAL
22F2013X-RAY DIFFRACTION6.069TORSIONAL
31B1994X-RAY DIFFRACTION6.069TORSIONAL
32E1994X-RAY DIFFRACTION6.069TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3001-3.38930.37651440.33142762290699
3.3893-3.4890.33821420.28892784292699
3.489-3.60160.31631430.25622744288799
3.6016-3.73030.26131420.246628082950100
3.7303-3.87960.30371230.242427932916100
3.8796-4.05610.28721490.24532808295799
4.0561-4.26980.29581380.227528082946100
4.2698-4.53720.18161310.170928042935100
4.5372-4.88730.21671510.15492795294699
4.8873-5.37870.22921490.17162810295999
5.3787-6.1560.23531440.198928552999100
6.156-7.7520.25911430.20482880302399
7.752-52.82070.21951200.17693009312999
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)
10.1935-0.6572-1.01264.66712.51242.13720.1582-0.0219-0.02550.1475-0.1541-0.04240.1216-0.27560.01860.29810.0442-0.10540.51980.02930.4652-194.2595146.4458-3.6219
21.8234-0.4995-0.71723.9821-0.59512.8779-0.168-0.2213-0.09460.050.1032-0.7072-0.03390.28790.04690.5121-0.04670.04820.4678-0.11920.5314-173.3196113.1824-22.8285
32.82271.86471.25055.42551.48841.90760.122-0.14020.02420.42240.0322-0.58660.20580.1427-0.11860.25610.109-0.06210.4892-0.05990.3989-184.1483181.569816.0529
44.8383-0.2477-1.04633.6338-0.26134.72880.0238-0.4559-0.25670.88440.1175-0.67530.0126-0.1728-0.09940.3662-0.0719-0.170.44280.03120.5341-200.7388207.29230.2724
56.3299-2.8905-0.21764.74941.14312.33650.113-0.17860.4637-0.0891-0.110.21980.0476-0.1809-0.03110.191-0.0387-0.00060.454-0.04460.3642-204.3707180.2816.9151
67.09363.80352.11186.04881.1031.86050.0612-0.0103-0.12550.216-0.13280.325-0.3081-0.12390.07730.23410.05940.04620.3741-0.02290.3271-207.4085215.46818.5049
70.3438-0.5804-0.72484.32272.23231.47880.13310.0066-0.03620.1924-0.24030.16310.168-0.27230.17480.3101-0.0036-0.04160.51090.04590.5272-142.0968146.90873.8862
82.1435-0.1008-0.48372.8327-0.42591.8370.0263-0.07310.0390.3539-0.020.0398-0.06420.0773-0.00910.4349-0.0455-0.00520.4106-0.08130.3639-121.7247113.681-16.4603
90.7311-0.23160.25273.73941.55741.3349-0.0092-0.09810.01910.15020.2118-0.17250.07880.2929-0.18330.1790.0041-0.01120.4088-0.00730.3442-131.3493182.931922.7859
103.77370.4024-0.59555.18840.20314.5220.1305-0.4857-0.42660.3890.075-0.2457-0.0375-0.0382-0.14630.2295-0.03950.01490.458-0.02450.3146-146.7808206.924936.8026
116.4774-2.0182-0.59743.23521.11812.08120.123-0.0396-0.0591-0.2143-0.26020.3936-0.1586-0.16610.15040.1823-0.0421-0.03740.397-0.05660.396-151.6855180.503214.1026
126.17064.34240.39868.46552.22631.3457-0.10.18250.2913-0.38160.07120.3461-0.3498-0.06110.02030.3260.0431-0.03640.38970.04570.2272-153.3954215.586425.5116
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 27:310)A27 - 310
2X-RAY DIFFRACTION2(chain A and resid 311:506)A311 - 506
3X-RAY DIFFRACTION3(chain B and resid 2:118)B2 - 118
4X-RAY DIFFRACTION4(chain B and resid 119:214)B119 - 214
5X-RAY DIFFRACTION5(chain C and resid 1:107)C1 - 107
6X-RAY DIFFRACTION6(chain C and resid 108:212)C108 - 212
7X-RAY DIFFRACTION7(chain D and resid 27:306)D27 - 306
8X-RAY DIFFRACTION8(chain D and resid 307:506)D307 - 506
9X-RAY DIFFRACTION9(chain E and resid 2:124)E2 - 124
10X-RAY DIFFRACTION10(chain E and resid 125:214)E125 - 214
11X-RAY DIFFRACTION11(chain F and resid 1:107)F1 - 107
12X-RAY DIFFRACTION12(chain F and resid 108:212)F108 - 212

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