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- PDB-7lvw: Structure of RSV F in Complex with VHH Cl184 -

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Basic information

Entry
Database: PDB / ID: 7lvw
TitleStructure of RSV F in Complex with VHH Cl184
Components
  • F-VHH-Cl184
  • Fusion glycoprotein F0
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / nanobody / VHH / antibody / fusion protein / virus complex / IMMUNE SYSTEM / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


symbiont-mediated induction of syncytium formation / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / host cell plasma membrane / virion membrane / plasma membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0
Similarity search - Domain/homology
Fusion glycoprotein F0
Similarity search - Component
Biological speciesRespiratory syncytial virus
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHsieh, C.-L. / McLellan, J.S.
CitationJournal: J.Virol. / Year: 2021
Title: A vulnerable, membrane-proximal site in human respiratory syncytial virus F revealed by a prefusion-specific single-domain antibody.
Authors: Rossey, I. / Hsieh, C.L. / Sedeyn, K. / Ballegeer, M. / Schepens, B. / Mclellan, J.S. / Saelens, X.
History
DepositionFeb 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fusion glycoprotein F0
G: F-VHH-Cl184
B: Fusion glycoprotein F0
C: Fusion glycoprotein F0
D: Fusion glycoprotein F0
E: Fusion glycoprotein F0
F: Fusion glycoprotein F0
I: F-VHH-Cl184
K: F-VHH-Cl184
L: F-VHH-Cl184
J: F-VHH-Cl184
H: F-VHH-Cl184
hetero molecules


Theoretical massNumber of molelcules
Total (without water)434,73521
Polymers433,30812
Non-polymers1,4279
Water40,6062254
1
A: Fusion glycoprotein F0
G: F-VHH-Cl184
B: Fusion glycoprotein F0
D: Fusion glycoprotein F0
I: F-VHH-Cl184
J: F-VHH-Cl184
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,78912
Polymers216,6546
Non-polymers1,1356
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23820 Å2
ΔGint-143 kcal/mol
Surface area73480 Å2
MethodPISA
2
C: Fusion glycoprotein F0
E: Fusion glycoprotein F0
F: Fusion glycoprotein F0
K: F-VHH-Cl184
L: F-VHH-Cl184
H: F-VHH-Cl184
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,9469
Polymers216,6546
Non-polymers2923
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23100 Å2
ΔGint-138 kcal/mol
Surface area72930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.490, 200.560, 134.660
Angle α, β, γ (deg.)90.000, 105.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Antibody , 2 types, 12 molecules ABCDEFGIKLJH

#1: Protein
Fusion glycoprotein F0 / Fusion glycoprotein F1 / Fusion glycoprotein F2


Mass: 55317.008 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Respiratory syncytial virus / Production host: Homo sapiens (human) / References: UniProt: W8RJF9
#2: Antibody
F-VHH-Cl184


Mass: 16900.924 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Cell line (production host): FreeStyle293 / Production host: Homo sapiens (human)

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Sugars , 2 types, 4 molecules

#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#4: 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.: 3 / Source method: obtained synthetically / 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 , 2 types, 2259 molecules

#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2254 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 3.13 Å3/Da / Density % sol: 60.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.2 M ammonium citrate pH 4.5, 12.5% (v/v) isopropanol, and 21% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.1→89.9 Å / Num. obs: 301087 / % possible obs: 97.4 % / Redundancy: 3.3 % / CC1/2: 0.989 / Net I/σ(I): 8.4
Reflection shellResolution: 2.1→2.14 Å / Num. unique obs: 15113 / CC1/2: 0.568

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C69

5c69


Resolution: 2.1→50.25 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2304 15057 5 %
Rwork0.201 285980 -
obs0.2025 301037 97.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.48 Å2 / Biso mean: 43.9403 Å2 / Biso min: 17.46 Å2
Refinement stepCycle: final / Resolution: 2.1→50.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28337 0 86 2254 30677
Biso mean--56.41 43.83 -
Num. residues----3670
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.120.29864670.284196721013998
2.12-2.150.29995560.275795501010698
2.15-2.180.27745210.263295711009298
2.18-2.20.31335320.269294681000098
2.2-2.230.29754560.26519511996797
2.23-2.260.29334860.26589389987596
2.26-2.290.29095030.27058996949993
2.29-2.330.29575030.26039369987296
2.33-2.370.27255000.239496701017099
2.37-2.40.28935110.248295891010098
2.4-2.450.27955260.239295691009598
2.45-2.490.28524990.244896591015898
2.49-2.540.26775510.249495441009598
2.54-2.590.28144860.235696501013698
2.59-2.650.26725330.228195591009298
2.65-2.710.26795170.231795071002497
2.71-2.780.27344570.22999240969794
2.78-2.850.24674730.2219258973195
2.85-2.930.26464940.223996701016499
2.93-3.030.26315090.21596731018299
3.03-3.140.23145250.208196661019199
3.14-3.260.23894730.205697201019398
3.26-3.410.23374970.196595781007598
3.41-3.590.20575010.18229362986395
3.59-3.820.20384830.17729342982595
3.82-4.110.20034940.174897721026699
4.11-4.520.18075230.158897181024199
4.52-5.180.1854820.15396681015098
5.18-6.520.20814820.18329420990295
6.52-50.250.18295170.165296201013797
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)
11.073-0.41890.05860.49160.06070.0243-0.00450.2185-0.1745-0.1779-0.0736-0.04370.0568-0.01270.07210.2739-0.04440.02650.18860.01460.2417-9.91115.33959.078
22.25590.1352-0.31747.3249-0.5972.58240.0306-0.07470.2266-0.0713-0.0009-0.1687-0.1837-0.0763-0.03540.21230.0357-0.00950.15660.06190.2596-11.14952.38866.218
30.3988-0.3416-0.1170.35730.21330.3370.0178-0.0075-0.004-0.01260.0435-0.06340.01170.1064-0.06280.21910.0007-0.00820.16070.01050.219-8.2963.4571.971
40.261-0.0501-0.29670.43120.03760.88530.0709-0.20520.00820.11690.00720.1481-0.003-0.0229-0.08660.30650.0025-0.00570.36610.00110.2341-36.18839.34117.722
51.1006-0.2168-0.52160.3830.28330.6037-0.0698-0.1129-0.13160.00590.0792-0.13610.080.102-0.00810.2752-0.0353-0.01710.2104-0.00240.2596-17.463-1.09856.968
61.23810.2707-0.29230.4257-0.31560.33750.056-0.43780.16050.25390.07620.1925-0.11010.0638-0.09860.33560.05930.00530.3893-0.03990.2398-42.99449.1864.043
70.6480.5247-0.61160.3452-0.17850.98580.1023-0.00820.1020.0041-0.02010.1488-0.014-0.2315-0.0710.3224-0.0165-0.03310.35330.01190.2573-44.9831.634.31
85.71341.90182.54332.97681.73675.6936-0.08760.28040.1182-0.38150.04570.3638-0.1038-0.17180.04390.313-0.0439-0.0620.1938-0.01810.3652-46.734-8.26734.64
92.29670.5474-0.60195.55440.6731.33470.05160.3599-1.3237-0.4949-0.15630.04751.04990.07930.10151.05290.0177-0.09820.4745-0.08880.8352-37.681-4.735-6.632
101.3854-0.53421.22221.5503-0.03293.709-0.0466-0.83250.44910.5993-0.0427-0.9594-0.34680.39110.05430.5472-0.135-0.18270.9556-0.08150.6791-5.75450.137.633
111.821-0.73730.53842.0709-2.48613.42270.1687-0.5657-0.11011.0172-0.11370.22950.186-0.1949-0.05650.7893-0.10340.02890.39990.05830.3062-16.231-13.008106.239
123.0208-0.45040.50884.9783-2.93066.320.0850.38160.2717-0.33-0.07140.0223-0.19430.10520.00320.26840.06020.0060.19670.02370.2851-41.72168.811-28.436
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 27:552 )A27 - 552
2X-RAY DIFFRACTION2( CHAIN G AND RESID 1:113 )G1 - 113
3X-RAY DIFFRACTION3( CHAIN B AND RESID 27:552 )B27 - 552
4X-RAY DIFFRACTION4( CHAIN C AND RESID 27:552 )C27 - 552
5X-RAY DIFFRACTION5( CHAIN D AND ( RESID 27:552 OR RESID 601:601 ) )D27 - 552
6X-RAY DIFFRACTION5( CHAIN D AND ( RESID 27:552 OR RESID 601:601 ) )D601
7X-RAY DIFFRACTION6( CHAIN E AND RESID 27:552 )E27 - 552
8X-RAY DIFFRACTION7( CHAIN F AND RESID 27:552 )F27 - 552
9X-RAY DIFFRACTION8( CHAIN I AND RESID 1:113 )I1 - 113
10X-RAY DIFFRACTION9( CHAIN K AND RESID 1:111 )K1 - 111
11X-RAY DIFFRACTION10( CHAIN L AND RESID 1:113 )L1 - 113
12X-RAY DIFFRACTION11( CHAIN J AND RESID 1:113 )J1 - 113
13X-RAY DIFFRACTION12( CHAIN H AND RESID 1:113 )H1 - 113

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