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- PDB-5w23: Crystal Structure of RSV F in complex with 5C4 Fab -

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Basic information

Entry
Database: PDB / ID: 5w23
TitleCrystal Structure of RSV F in complex with 5C4 Fab
Components
  • 5C4 Fab heavy chain
  • 5C4 Fab light chain
  • Fusion glycoprotein F0
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / RSV / Complex / Fab / Antibody / Neutralizing antibody / 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
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
Model detailsThe fusion inhibitor JNJ-2408068 has an occupancy of 0.33 in the asymmetric unit
AuthorsBattles, M.B. / McLellan, J.S.
CitationJournal: Nat Commun / Year: 2017
Title: Structural basis of respiratory syncytial virus subtype-dependent neutralization by an antibody targeting the fusion glycoprotein.
Authors: Tian, D. / Battles, M.B. / Moin, S.M. / Chen, M. / Modjarrad, K. / Kumar, A. / Kanekiyo, M. / Graepel, K.W. / Taher, N.M. / Hotard, A.L. / Moore, M.L. / Zhao, M. / Zheng, Z.Z. / Xia, N.S. / ...Authors: Tian, D. / Battles, M.B. / Moin, S.M. / Chen, M. / Modjarrad, K. / Kumar, A. / Kanekiyo, M. / Graepel, K.W. / Taher, N.M. / Hotard, A.L. / Moore, M.L. / Zhao, M. / Zheng, Z.Z. / Xia, N.S. / McLellan, J.S. / Graham, B.S.
History
DepositionJun 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
H: 5C4 Fab heavy chain
L: 5C4 Fab light chain
I: 5C4 Fab heavy chain
M: 5C4 Fab light chain
J: 5C4 Fab heavy chain
N: 5C4 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)350,08617
Polymers349,5639
Non-polymers5238
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)183.360, 183.360, 275.900
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
11chain A
21(chain B and resid 27 through 510)
31(chain C and resid 27 through 510)
12chain H
22chain I
32chain J
13(chain L and resid 1 through 211)
23chain M
33chain N

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNASPASPchain AAA27 - 51027 - 510
21ASNASNASPASP(chain B and resid 27 through 510)BB27 - 51027 - 510
31ASNASNASPASP(chain C and resid 27 through 510)CC27 - 51027 - 510
12VALVALARGARGchain HHD2 - 21325 - 247
22VALVALARGARGchain IIF2 - 21325 - 247
32VALVALARGARGchain JJH2 - 21325 - 247
13ASPASPARGARG(chain L and resid 1 through 211)LE1 - 21124 - 238
23ASPASPARGARGchain MMG1 - 21124 - 238
33ASPASPARGARGchain NNI1 - 21124 - 238

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Fusion glycoprotein F0 / Protein F


Mass: 63112.094 Da / Num. of mol.: 3 / Fragment: UNP residues 1-513
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A / Strain: A2 / Production host: Homo sapiens (human) / References: UniProt: P03420
#2: Antibody 5C4 Fab heavy chain


Mass: 26678.139 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/c / Plasmid: PVRC8400 / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#3: Antibody 5C4 Fab light chain


Mass: 26730.689 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/c / Plasmid: PVRC8400 / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: Zn

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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: 3.57 Å3/Da / Density % sol: 65.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Seed stock: 0.01 M zinc sulfate heptahydrate, 0.1 M MES hydrate pH 6.5, 22.5% v/v PEG MME 550 and 0.5% w/v polyvinylpyrrolidone K15 Reservoir solution: 0.2 M ammonium acetate, 0.1 M BIS-TRIS ...Details: Seed stock: 0.01 M zinc sulfate heptahydrate, 0.1 M MES hydrate pH 6.5, 22.5% v/v PEG MME 550 and 0.5% w/v polyvinylpyrrolidone K15 Reservoir solution: 0.2 M ammonium acetate, 0.1 M BIS-TRIS pH 6.5 and 25% PEG 3350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.4→34.06 Å / Num. obs: 64552 / % possible obs: 99.1 % / Redundancy: 7.3 % / Biso Wilson estimate: 64.99 Å2 / CC1/2: 0.968 / Rmerge(I) obs: 0.38 / Rpim(I) all: 0.14 / Rrim(I) all: 0.406 / Net I/σ(I): 7.4 / Num. measured all: 470679 / Scaling rejects: 168
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
3.4-3.487.21.5960.4620.5851.70799.2
15.58-34.065.80.0730.9920.0330.08187.4

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
MOSFLMdata reduction
Aimless0.5.17data scaling
PDB_EXTRACT3.22data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C69, 4MMS

5c69

4mms


Resolution: 3.4→34.06 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.57
RfactorNum. reflection% reflection
Rfree0.2389 3270 5.08 %
Rwork0.1978 --
obs0.1999 64427 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 175.38 Å2 / Biso mean: 63.2723 Å2 / Biso min: 20.92 Å2
Refinement stepCycle: final / Resolution: 3.4→34.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20304 0 8 0 20312
Biso mean--106.06 --
Num. residues----2646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00720724
X-RAY DIFFRACTIONf_angle_d1.05328203
X-RAY DIFFRACTIONf_chiral_restr0.0573329
X-RAY DIFFRACTIONf_plane_restr0.0063568
X-RAY DIFFRACTIONf_dihedral_angle_d11.71712594
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6341X-RAY DIFFRACTION9.885TORSIONAL
12B6341X-RAY DIFFRACTION9.885TORSIONAL
13C6341X-RAY DIFFRACTION9.885TORSIONAL
21H2994X-RAY DIFFRACTION9.885TORSIONAL
22I2994X-RAY DIFFRACTION9.885TORSIONAL
23J2994X-RAY DIFFRACTION9.885TORSIONAL
31L3073X-RAY DIFFRACTION9.885TORSIONAL
32M3073X-RAY DIFFRACTION9.885TORSIONAL
33N3073X-RAY DIFFRACTION9.885TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4-3.45070.37911350.32552638277398
3.4507-3.50460.31191430.29132597274099
3.5046-3.5620.33671330.27092625275899
3.562-3.62340.31931310.26582637276899
3.6234-3.68920.28411730.24572606277999
3.6892-3.76010.28981410.24962636277799
3.7601-3.83670.30691370.244226432780100
3.8367-3.920.29291440.242926362780100
3.92-4.01110.25361250.2332654277999
4.0111-4.11120.28021290.205726682797100
4.1112-4.22220.23521290.19222660278999
4.2222-4.34620.17961450.17142651279699
4.3462-4.48620.18161280.16492674280299
4.4862-4.64610.20051500.15432626277699
4.6461-4.83160.19181480.15412667281599
4.8316-5.05090.21341660.15282638280499
5.0509-5.31620.2121590.16432640279999
5.3162-5.64790.2341410.18172670281199
5.6479-6.08170.23491450.19162672281799
6.0817-6.68960.24361560.19492673282998
6.6896-7.6480.23351330.192707284098
7.648-9.59980.21111420.15362713285598
9.5998-34.06540.18381370.17442826296396
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)
11.8906-0.11580.6241.8066-0.68812.33180.2787-0.284-0.50250.0088-0.4195-0.30930.40990.27340.13490.3304-0.13040.03330.42690.16190.462105.47791.5002298.6748
21.88540.51740.25391.23980.06211.57230.1355-0.52470.08290.2409-0.3308-0.2495-0.18340.25480.16450.4068-0.16740.02990.58790.10280.3359111.109522.0861303.0372
31.23280.64450.15721.22480.12811.07540.3223-0.6481-0.07510.4227-0.3802-0.1592-0.08110.24840.05950.5551-0.38120.03160.82940.04130.406697.126611.8402316.0706
43.9835-0.99123.22043.32860.26043.2279-0.32550.97090.4155-0.62890.1975-0.4559-0.08490.47270.14841.049-0.4987-0.1180.80080.06110.631350.078-33.5473252.0998
51.41071.09080.77532.10140.91640.872-0.35030.3510.3189-0.51690.25020.4378-0.0673-0.0720.03031.1838-0.6031-0.53070.4261-0.0390.646934.0501-33.3745254.5793
66.74261.99130.17244.08730.77014.61310.19810.199-1.11470.18210.17140.52890.935-0.2527-0.37830.56270.0577-0.13080.27220.00290.670425.918947.3292321.7495
75.0917-1.2292-2.1212.26750.50885.17150.13220.2733-0.2563-0.0637-0.09820.3595-0.0595-0.461-0.10420.19980.003-0.07690.3726-0.02410.458819.552861.162316.1749
88.2101-3.12371.92237.8528-2.53194.9544-0.2817-0.40871.03930.2384-0.3236-0.51-1.40.3730.5071.0117-0.041-0.12970.46880.06650.562486.937265.7838234.2773
93.84020.76590.26054.1795-1.53565.3749-0.28390.40870.2948-0.2462-0.0271-0.5749-1.25730.23720.24930.7930.06830.00120.37970.08780.602681.707161.349219.6518
102.4694-0.45510.9432.4591-1.2492.91230.2376-0.17170.1307-0.1737-0.34240.0342-0.0195-0.02830.09080.2602-0.14450.06890.2799-0.12780.175396.763315.7605286.8987
113.04040.29170.67391.096-0.29941.68180.1406-0.70120.26250.0969-0.35240.3483-0.2594-0.18230.16470.4846-0.12720.10830.4131-0.05270.388291.614626.0835300.5285
121.9660.63830.87971.16360.27612.23940.2282-0.293-0.009-0.0039-0.19330.0754-0.0420.12380.06020.3333-0.25780.21960.5206-0.02910.288985.61979.7718300.2093
133.02610.3586-0.17147.759-1.6214.3953-0.12140.3418-0.1715-0.44110.0587-0.37760.14260.22750.06180.209-0.05910.08120.3583-0.10470.307963.9237-17.1078276.9149
144.42740.0251-1.47213.78021.89985.1507-0.0303-0.3799-0.47390.11990.2017-0.47610.34040.5385-0.13550.41440.2107-0.05860.3886-0.02040.453456.253843.906315.9399
156.90972.026-1.65776.6617-2.16676.8675-0.12020.09440.80110.2317-0.0082-0.4955-0.44160.74890.10750.2564-0.0003-0.10010.3859-0.01730.438597.946943.6802252.7748
164.57851.72182.44523.43811.0555.3743-0.1555-0.06110.6039-0.5506-0.00641.1495-0.2829-0.38620.22170.485-0.1028-0.11870.2793-0.01240.698147.9217-2.8896272.207
176.4596-0.73060.18493.36440.30954.04270.09970.64920.1711-0.5898-0.1909-0.1737-0.09060.03910.08440.53520.10690.08380.3331-0.07410.338450.006450.5536295.9693
184.635-1.04561.05654.2514-1.06485.43040.06760.2017-0.0842-0.04190.00460.14770.1831-0.1369-0.05340.2940.07780.01030.1961-0.04930.329479.237733.9754246.6878
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 137 through 510)A137 - 510
2X-RAY DIFFRACTION2(chain 'B' and resid 137 through 512)B137 - 512
3X-RAY DIFFRACTION3(chain 'C' and resid 137 through 512)C137 - 512
4X-RAY DIFFRACTION4(chain 'H' and resid 113 through 213)H113 - 213
5X-RAY DIFFRACTION5(chain 'L' and resid 109 through 212)L109 - 212
6X-RAY DIFFRACTION6(chain 'I' and resid 113 through 213)I113 - 213
7X-RAY DIFFRACTION7(chain 'M' and resid 109 through 211)M109 - 211
8X-RAY DIFFRACTION8(chain 'J' and resid 113 through 213)J113 - 213
9X-RAY DIFFRACTION9(chain 'N' and resid 109 through 211)N109 - 211
10X-RAY DIFFRACTION10(chain 'A' and resid 27 through 98)A27 - 98
11X-RAY DIFFRACTION11(chain 'B' and resid 27 through 98)B27 - 98
12X-RAY DIFFRACTION12(chain 'C' and resid 26 through 98)C26 - 98
13X-RAY DIFFRACTION13(chain 'H' and resid 2 through 112)H2 - 112
14X-RAY DIFFRACTION14(chain 'I' and resid 2 through 112)I2 - 112
15X-RAY DIFFRACTION15(chain 'J' and resid 2 through 112)J2 - 112
16X-RAY DIFFRACTION16(chain 'L' and resid 1 through 108)L1 - 108
17X-RAY DIFFRACTION17(chain 'M' and resid 1 through 108)M1 - 108
18X-RAY DIFFRACTION18(chain 'N' and resid 1 through 108)N1 - 108

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