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- PDB-6w52: Prefusion RSV F bound by neutralizing antibody RSB1 -

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Basic information

Entry
Database: PDB / ID: 6w52
TitlePrefusion RSV F bound by neutralizing antibody RSB1
Components
  • Fusion glycoprotein F0
  • Fusion glycoprotein F1 fused with Fibritin trimerization domain
  • RSB1 Fab Heavy Chain
  • RSB1 Fab Light Chain
KeywordsVIRAL PROTEIN / RSV / antibody / neutralization / prefusion / vaccine
Function / homology
Function and homology information


positive regulation of syncytium formation by virus / host cell Golgi membrane / 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 / membrane / identical protein binding / plasma membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Fibritin C-terminal / Fibritin C-terminal region
Similarity search - Domain/homology
Fusion glycoprotein F0 / Fibritin / Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respiratory syncytial virus A
Escherichia phage T2 (virus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.74 Å
AuthorsHarshbarger, W. / Chandramouli, S. / Malito, M.
CitationJournal: Plos Pathog. / Year: 2020
Title: Convergent structural features of respiratory syncytial virus neutralizing antibodies and plasticity of the site V epitope on prefusion F.
Authors: Harshbarger, W. / Tian, S. / Wahome, N. / Balsaraf, A. / Bhattacharya, D. / Jiang, D. / Pandey, R. / Tungare, K. / Friedrich, K. / Mehzabeen, N. / Biancucci, M. / Chinchilla-Olszar, D. / ...Authors: Harshbarger, W. / Tian, S. / Wahome, N. / Balsaraf, A. / Bhattacharya, D. / Jiang, D. / Pandey, R. / Tungare, K. / Friedrich, K. / Mehzabeen, N. / Biancucci, M. / Chinchilla-Olszar, D. / Mallett, C.P. / Huang, Y. / Wang, Z. / Bottomley, M.J. / Malito, E. / Chandramouli, S.
History
DepositionMar 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 F1 fused with Fibritin trimerization domain
H: RSB1 Fab Heavy Chain
L: RSB1 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)109,9394
Polymers109,9394
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13470 Å2
ΔGint-92 kcal/mol
Surface area39490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.298, 190.298, 190.298
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Space group name HallI2b2c3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z+1/2,x
#5: z,-x,-y+1/2
#6: -y+1/2,z,-x
#7: -z,-x+1/2,y
#8: -z+1/2,x,-y
#9: y,-z,-x+1/2
#10: x,-y,-z+1/2
#11: -x+1/2,y,-z
#12: -x,-y+1/2,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1,x+1/2
#17: z+1/2,-x+1/2,-y+1
#18: -y+1,z+1/2,-x+1/2
#19: -z+1/2,-x+1,y+1/2
#20: -z+1,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1
#22: x+1/2,-y+1/2,-z+1
#23: -x+1,y+1/2,-z+1/2
#24: -x+1/2,-y+1,z+1/2

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Components

#1: Protein Fusion glycoprotein F0 / Protein F


Mass: 9215.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A (strain A2)
Strain: A2 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P03420
#2: Protein Fusion glycoprotein F1 fused with Fibritin trimerization domain


Mass: 45609.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A, (gene. exp.) Escherichia phage T2 (virus)
Gene: F, MZ07_64446gpF, wac / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: A0A2H4WLA4, UniProt: A0A2Z5WL46, UniProt: P03420*PLUS
#3: Antibody RSB1 Fab Heavy Chain


Mass: 29977.432 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody RSB1 Fab Light Chain


Mass: 25137.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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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: 2.61 Å3/Da / Density % sol: 52.91 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Hepes pH 7.5, 25% PEG 2000 MME, 0.01 M spermidine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.74→50 Å / Num. obs: 11995 / % possible obs: 99.77 % / Redundancy: 11.2 % / Biso Wilson estimate: 25.69 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.0956 / Net I/σ(I): 20.79
Reflection shellResolution: 3.74→3.8 Å / Num. unique obs: 1188 / CC1/2: 0.919

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MMU

4mmu


Resolution: 3.74→40.57 Å / SU ML: 0.4256 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.5636
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2863 1198 9.99 %
Rwork0.218 10789 -
obs0.2251 11987 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.83 Å2
Refinement stepCycle: LAST / Resolution: 3.74→40.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6632 0 0 0 6632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00216759
X-RAY DIFFRACTIONf_angle_d0.56699190
X-RAY DIFFRACTIONf_chiral_restr0.04281082
X-RAY DIFFRACTIONf_plane_restr0.00451161
X-RAY DIFFRACTIONf_dihedral_angle_d16.3698924
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.74-3.890.31031330.24151186X-RAY DIFFRACTION99.77
3.89-4.070.35411320.2461177X-RAY DIFFRACTION100
4.07-4.280.25851320.2221176X-RAY DIFFRACTION100
4.28-4.550.29651350.1871192X-RAY DIFFRACTION100
4.55-4.90.27381320.19211204X-RAY DIFFRACTION100
4.9-5.390.2961270.21291196X-RAY DIFFRACTION100
5.4-6.170.34171350.24291195X-RAY DIFFRACTION100
6.17-7.760.26571330.23561213X-RAY DIFFRACTION100
7.77-40.570.22741390.20531250X-RAY DIFFRACTION99.29
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)
10.84444450862-0.509056275587-0.0931443635220.6276342865120.1248684558230.4076529689-0.186835664271-0.3617318497270.5955525863480.2339696409850.162427117143-0.4022823505550.1013618339680.4372584216810.1451971145970.2210382884420.2568447311940.02735660177570.6516169101550.1484021108490.697152328756-9.36316370262-17.4247779196-32.2887660648
22.773879620651.21519366217-0.757556031511.42246600901-0.3756142812381.508300981020.2637220329070.1757588707560.3301036628870.418013784172-0.4207898146480.485695557826-0.0179415949075-0.741659217920.1311839682120.690559122688-0.177402070210.4434324014621.097740701410.1426455698771.2006043522-82.0369402098-24.0849677901-20.671593542
34.042889799522.21606554813-0.9771002505311.490107214130.3257698919082.93100576086-0.06355169722730.0102727483493-0.2176891682890.074872030248-0.08705001188750.484384492671-0.0273924400182-0.4821332815860.1683815356090.2984478440960.01785252191710.2508029498130.8680886675680.02949761460090.856742335507-76.4376650005-24.053300956-30.5738411429
43.00803627959-3.25594552302-2.186669046686.452651336092.239731451394.643666808590.1298970679740.03759732417060.6016169056080.137287666374-0.08695226054450.595898722908-0.523001264787-0.799218842799-0.06873632944020.4030815136420.1153798597670.289858862170.7973736862040.03219818208530.682459565847-73.8696066334-17.2965683179-30.3085028325
58.50822546289-5.565120866751.405096842674.748169647050.007432096643571.05716182990.105145793691-0.453225246071.351659646750.125166805164-0.0046803296752-0.253973731537-0.532554562952-0.498454003946-0.1549108849710.5006465035490.1129475329620.3450518262540.679655911257-0.03606966264170.738246665689-70.0830389423-14.1499754474-26.835446376
63.26206464186-0.7982042105910.8834342789581.30633936974-0.8824188725351.42790358441-0.292244440842-0.5372198130160.1857695483510.342272265390.379234603070.304938298248-0.190222093942-0.424293788726-0.07053667636240.5560289854960.1048788385730.3479083904091.10461812621-0.2047520775861.0504141042-77.8635743312-18.6267082739-21.0757403023
70.2564507254820.49907066135-0.336432724411.02063149373-0.7516156754810.632179354042-0.0463523602955-0.281043057891-0.2030453523740.333342500515-0.2504691520270.4424796543050.237724046894-0.6075505136990.3035651265560.269553417491-0.08317282231930.167335631270.7435402453840.09494608248830.746227915942-72.3025739026-25.8279250652-35.655578149
84.11934926728-0.8726710718590.3385558504973.741967895-0.3662823444090.324638036506-0.284872716153-0.592978974081-0.07922591732610.4883463727420.02793667203070.561689567710.1181996661340.03280256212230.2374931304230.38623861115-0.1302240466380.1548656709021.40733834695-0.04577631808531.3201303417-86.0403252494-22.4592069004-25.6830338918
93.74446911490.9374169507841.459338642521.792206255930.8320624976792.139716089270.05525975027760.225928710134-0.409185527277-0.0469155282823-0.02081582664530.7301462061130.0114625362306-0.96475821101-0.0903484045940.500863427150.294139820915-0.1943302815611.266236550450.06731381072211.44142883585-87.0813184441-16.0423059686-50.677812346
104.523055871771.11201921479-1.249779432041.520853469930.0694895868362.75092327229-0.116757389054-0.0137306372349-0.315053000620.126570598094-0.1241482298650.4878075820180.140190806045-0.7637172054220.1819254705580.2291986803930.03121946624810.01366633630410.7917979741790.1092464106610.937600070648-77.7962914857-19.4601349626-43.6054933537
114.89818560907-1.72283644643-3.613735470039.022923169050.1088278910912.84904013-0.1505932942770.194107273223-0.3182742197120.2794181832180.2008856090020.6763909432320.387559335015-0.872637321021-0.04610593605890.587222851227-0.2354011694750.06915037930520.7564394908730.05190399013840.915057425883-75.6948952056-27.0543002003-47.6910654964
126.228610581452.66233658898-2.384014039211.13797208647-1.01903772330.912480842395-0.02649383209260.709701645132-0.0367643353527-0.701958447080.1312299313020.9123388471740.350261888832-1.7918774862-0.1086138991620.800713054449-0.106817643035-0.552885899631.29819305097-0.09986091278141.46259337491-80.6592097458-31.7659497172-52.217438934
133.78067380823.177213565532.053968563373.386680427021.599165328273.387478633620.06785432319170.394670272781-0.0311572772592-0.2683624070050.004581662503251.535117380040.12773438374-1.11522240903-0.08722121808840.4464668513510.199149410162-0.1857165448441.117701584360.1236191454961.28447694592-82.5944381497-21.3445904647-49.5578658855
140.169438024960.0705611637101-0.273255348221.32218987775-0.6528074877670.6652244566290.1074637618990.6224614334560.210052175773-0.301485567088-0.05365398647851.285129597540.351148218576-0.883215610547-0.07917749608680.354729212095-0.0177736121625-0.001082573703141.24121558301-0.06484649971481.14861938668-86.0996825658-19.6125603357-44.1291581379
155.21920156657-1.050719736045.292405841837.825061788040.2297673072085.587048590640.3128195257611.673449602540.951103380974-0.604065141817-0.3852627676590.6656090181490.06413891395521.004344025820.09229178227050.4298883860930.277388497950.1843949057410.8672181463640.3107812148130.86297880332-2.95677657614-17.6996056607-44.7274341746
161.08267423052-0.1490037469240.2640662799190.8340340117350.4923557325081.123742626280.002351037472350.04173417232930.135201086504-0.01458839206080.111971618011-0.1396466003660.05057764844590.415687685346-0.08207587065110.2338167371840.08346235811770.1179486601510.5064640409840.2481681075860.629454376835-13.7348152389-14.366526911-40.6509165574
173.14081198623.06832610295-0.5065517120315.08322198408-1.565719369572.18040768346-0.1024067683170.2190847097650.184507383146-0.1449164205540.1822604729070.14591723232-0.0376869509847-0.122677509641-0.05274597152340.1684262056990.09781993412050.06557098319590.1415588230870.06405094075090.0953281279801-49.4645503427-21.3056326336-46.6967447886
186.59427636515-7.05050994465-6.263994910188.458035764798.091199607638.062519533560.331644490491-1.08214458665-2.794367204841.3070335887-0.4606322000972.869641045432.71426774666-1.966051780750.1293487766320.600640130377-0.235888520702-0.08566716116030.6418176459470.1716873858370.948559532424-67.6374344221-36.2334548096-41.9483292706
192.143752953181.942424903351.973709866122.01693647181.905211202859.521462063021.392623995541.39416184122.5489010084-3.52266908017-0.770559425973-2.8189869176-1.44640383645-0.360760847669-0.6259727486431.36684867670.002295779926870.114019607940.8849597813910.09869197496381.14211859293-68.544550727-50.6521982684-42.8364290661
204.533877950170.284047525981-1.056314076270.8986831952471.550530626026.0177379471-0.08914486532830.0209820367399-0.6628835385720.135863749116-0.0201132917624-0.05454326295090.610571864085-0.4858513599340.1767042522130.1586229308470.01286150861760.09259344230220.2304559810130.1745833678620.32013871042-57.6976120722-38.6486604772-38.798736024
210.624717729975-1.01168322635-0.3290793155172.23727887235-0.3353603540981.42298306050.02721654183770.1078289378270.104347488352-0.119786874674-0.08046632640530.1150633463180.006998158070130.008851257865020.0008149750944940.1130603174970.1044101698630.03478965741130.2131483559420.1172682839620.169513817063-47.3372109821-24.9032510393-46.6309264343
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 277 through 509 )
2X-RAY DIFFRACTION2chain 'H' and (resid 1 through 23 )
3X-RAY DIFFRACTION3chain 'H' and (resid 24 through 45 )
4X-RAY DIFFRACTION4chain 'H' and (resid 46 through 52 )
5X-RAY DIFFRACTION5chain 'H' and (resid 52A through 66 )
6X-RAY DIFFRACTION6chain 'H' and (resid 67 through 89 )
7X-RAY DIFFRACTION7chain 'H' and (resid 90 through 101 )
8X-RAY DIFFRACTION8chain 'H' and (resid 102 through 113 )
9X-RAY DIFFRACTION9chain 'L' and (resid 1 through 24 )
10X-RAY DIFFRACTION10chain 'L' and (resid 25 through 44 )
11X-RAY DIFFRACTION11chain 'L' and (resid 45 through 53 )
12X-RAY DIFFRACTION12chain 'L' and (resid 54 through 63 )
13X-RAY DIFFRACTION13chain 'L' and (resid 64 through 93 )
14X-RAY DIFFRACTION14chain 'L' and (resid 94 through 109 )
15X-RAY DIFFRACTION15chain 'A' and (resid 26 through 33 )
16X-RAY DIFFRACTION16chain 'A' and (resid 34 through 52 )
17X-RAY DIFFRACTION17chain 'A' and (resid 53 through 62 )
18X-RAY DIFFRACTION18chain 'A' and (resid 63 through 67 )
19X-RAY DIFFRACTION19chain 'A' and (resid 68 through 73 )
20X-RAY DIFFRACTION20chain 'A' and (resid 74 through 97 )
21X-RAY DIFFRACTION21chain 'B' and (resid 137 through 276 )

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