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- PDB-4jhw: Crystal Structure of Respiratory Syncytial Virus Fusion Glycoprot... -

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Basic information

Entry
Database: PDB / ID: 4jhw
TitleCrystal Structure of Respiratory Syncytial Virus Fusion Glycoprotein Stabilized in the Prefusion Conformation by Human Antibody D25
Components
  • D25 antigen-binding fragment heavy chain
  • D25 light chain
  • Fusion glycoprotein F0
KeywordsIMMUNE SYSTEM / immunoglobulin / type I fusion protein / membrane fusion
Function / homology
Function and homology information


symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / 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 ...symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / 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 speciesHomo sapiens (human)
Human respiratory syncytial virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsMclellan, J.S. / Chen, M. / Leung, S. / Graepel, K.W. / Du, X. / Yang, Y. / Zhou, T. / Baxa, U. / Yasuda, E. / Beaumont, T. ...Mclellan, J.S. / Chen, M. / Leung, S. / Graepel, K.W. / Du, X. / Yang, Y. / Zhou, T. / Baxa, U. / Yasuda, E. / Beaumont, T. / Kumar, A. / Modjarrad, K. / Zheng, Z. / Zhao, M. / Xia, N. / Kwong, P.D. / Graham, B.S.
CitationJournal: Science / Year: 2013
Title: Structure of RSV fusion glycoprotein trimer bound to a prefusion-specific neutralizing antibody.
Authors: McLellan, J.S. / Chen, M. / Leung, S. / Graepel, K.W. / Du, X. / Yang, Y. / Zhou, T. / Baxa, U. / Yasuda, E. / Beaumont, T. / Kumar, A. / Modjarrad, K. / Zheng, Z. / Zhao, M. / Xia, N. / ...Authors: McLellan, J.S. / Chen, M. / Leung, S. / Graepel, K.W. / Du, X. / Yang, Y. / Zhou, T. / Baxa, U. / Yasuda, E. / Beaumont, T. / Kumar, A. / Modjarrad, K. / Zheng, Z. / Zhao, M. / Xia, N. / Kwong, P.D. / Graham, B.S.
History
DepositionMar 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 20, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 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
H: D25 antigen-binding fragment heavy chain
L: D25 light chain
F: Fusion glycoprotein F0


Theoretical massNumber of molelcules
Total (without water)102,7163
Polymers102,7163
Non-polymers00
Water00
1
H: D25 antigen-binding fragment heavy chain
L: D25 light chain
F: Fusion glycoprotein F0

H: D25 antigen-binding fragment heavy chain
L: D25 light chain
F: Fusion glycoprotein F0

H: D25 antigen-binding fragment heavy chain
L: D25 light chain
F: Fusion glycoprotein F0


Theoretical massNumber of molelcules
Total (without water)308,1489
Polymers308,1489
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_564z,x+1,y-11
crystal symmetry operation9_465y-1,z+1,x1
Buried area29540 Å2
ΔGint-170 kcal/mol
Surface area104890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.286, 152.286, 152.286
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Antibody D25 antigen-binding fragment heavy chain


Mass: 24375.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK293 / Production host: homo sapiens (human)
#2: Antibody D25 light chain


Mass: 23325.865 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK293 / Production host: homo sapiens (human)
#3: Protein Fusion glycoprotein F0 / Protein F / Fusion glycoprotein F2 / Fusion glycoprotein F1


Mass: 55014.629 Da / Num. of mol.: 1 / Mutation: P102A, I379V, M447V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus / Strain: A2 / Gene: F, fusion glycoprotein / Plasmid: paH / Cell line (production host): HEK293 / Production host: homo sapiens (human) / References: UniProt: P03420
Has protein modificationY
Sequence detailsAUTHOR STATES THAT THE ORF FOR THE CRYSTALLIZED RSV F PROTEIN IS: ...AUTHOR STATES THAT THE ORF FOR THE CRYSTALLIZED RSV F PROTEIN IS: MELLILKANAITTILTAVTFCFASGQNITEEFYQSTCSAVSKGYLSALRTGWYTSVITIELSNIKENKCNGTDAKVKLIKQELDKYKNAVTELQLLMQSTPATNNRARRELPRFMNYTLNNAKKTNVTLSKKRKRRFLGFLLGVGSAIASGVAVSKVLHLEGEVNKIKSALLSTNKAVVSLSNGVSVLTSKVLDLKNYIDKQLLPIVNKQSCSISNIETVIEFQQKNNRLLEITREFSVNAGVTTPVSTYMLTNSELLSLINDMPITNDQKKLMSNNVQIVRQQSYSIMSIIKEEVLAYVVQLPLYGVIDTPCWKLHTSPLCTTNTKEGSNICLTRTDRGWYCDNAGSVSFFPQAETCKVQSNRVFCDTMNSLTLPSEVNLCNVDIFNPKYDCKIMTSKTDVSSSVITSLGAIVSCYGKTKCTASNKNRGIIKTFSNGCDYVSNKGVDTVSVGNTLYYVNKQEGKSLYVKGEPIINFYDPLVFPSDEFDASISQVNEKINQSLAFIRKSDELLSAIGGYIPEAPRDGQAYVRKDGEWVLLSTFLGGLVPRGSHHHHHHSAWSHPQFEK. THE N-TERMINAL, C-TERMINAL, AND 27 INTERVENING RESIDUES ARE NOT PRESENT IN THE MATURE PROTEIN DUE EITHER TO CELLULAR PROTEASES OR THROMBIN TREATMENT. THE SEQUENCE OF THE MATURE PROTEIN THAT WAS CRYSTALLIZED IS: QNITEEFYQSTCSAVSKGYLSALRTGWYTSVITIELSNIKENKCNGTDAKVKLIKQELDKYKNAVTELQLLMQSTPATNNRARRFLGFLLGVGSAIASGVAVSKVLHLEGEVNKIKSALLSTNKAVVSLSNGVSVLTSKVLDLKNYIDKQLLPIVNKQSCSISNIETVIEFQQKNNRLLEITREFSVNAGVTTPVSTYMLTNSELLSLINDMPITNDQKKLMSNNVQIVRQQSYSIMSIIKEEVLAYVVQLPLYGVIDTPCWKLHTSPLCTTNTKEGSNICLTRTDRGWYCDNAGSVSFFPQAETCKVQSNRVFCDTMNSLTLPSEVNLCNVDIFNPKYDCKIMTSKTDVSSSVITSLGAIVSCYGKTKCTASNKNRGIIKTFSNGCDYVSNKGVDTVSVGNTLYYVNKQEGKSLYVKGEPIINFYDPLVFPSDEFDASISQVNEKINQSLAFIRKSDELLSAIGGYIPEAPRDGQAYVRKDGEWVLLSTFLGGLVPR. THE CRYSTALLIZED PROTEIN IS A VARIANT OF UNP P03420 (FUS_HRSVA) SEQUENCE CONTAINING THREE AMINO ACID SUBSTITUTIONS (P102A, I379V, AND M447V).

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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: 2.87 Å3/Da / Density % sol: 57.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% (w/v) PEG 400, 3.75% (w/v) PEG 3350, 0.1 M HEPES pH 7.5, and 1% (v/v) 1,2-butanediol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 19, 2012
RadiationMonochromator: Si 111. Rosenbaum-Rock double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. all: 13953 / Num. obs: 13898 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 3.6→3.73 Å / Redundancy: 5.2 % / % possible all: 99.3

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RRR AND 4JHA

3rrr

4jha


Resolution: 3.6→42.237 Å / SU ML: 0.51 / σ(F): 1.35 / Phase error: 32.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2671 671 4.84 %Random
Rwork0.213 ---
all0.2157 13877 --
obs0.2157 13877 99.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.6→42.237 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6778 0 0 0 6778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036914
X-RAY DIFFRACTIONf_angle_d0.9089385
X-RAY DIFFRACTIONf_dihedral_angle_d13.7292513
X-RAY DIFFRACTIONf_chiral_restr0.061112
X-RAY DIFFRACTIONf_plane_restr0.0041190
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.87720.33591300.28232612X-RAY DIFFRACTION99
3.8772-4.2670.33841380.25122612X-RAY DIFFRACTION100
4.267-4.88370.25831270.19552627X-RAY DIFFRACTION100
4.8837-6.14990.2731550.23812630X-RAY DIFFRACTION100
6.1499-42.23940.24231210.19222725X-RAY DIFFRACTION99
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)
18.68650.94071.20515.87630.1162.45610.06720.4987-0.95870.17690.3322-0.58280.80220.0138-0.37681.05060.07040.0680.6092-0.09140.61618.8979127.504310.9437
25.3929-1.62820.04224.7467-2.48492.1190.19251.3722-1.1346-0.8887-0.0858-0.37012.176-0.5366-0.16491.9971-0.1557-0.11071.359-0.46651.4378-10.2047105.2518-6.0292
31.52420.29360.96394.07593.57673.55530.1365-0.36460.0202-0.03060.0531-0.51080.0523-0.2529-0.24260.621-0.09620.21030.82430.13180.674922.1107171.823337.8653
42.48073.74561.61234.50234.38376.2946-0.26460.1643-0.26350.35290.0219-0.40710.68310.68720.33470.76030.2417-0.03940.6710.12021.029924.01156.557925.5589
52.8897-0.15161.61357.93043.22053.84520.4091-0.5478-0.29441.1057-0.35750.63071.1094-0.85020.15580.8397-0.06040.07620.9310.23030.620422.6164167.68242.3761
67.28047.4154-1.18422.1291-2.26747.02790.222-0.34640.5607-0.635-0.19431.7419-0.17630.44060.10050.66340.1382-0.06840.9057-0.12861.004428.5106194.246850.1069
73.7512-0.4022-0.53314.2173-1.130.255-0.0023-0.54130.50280.00470.1046-0.1025-0.36060.3096-0.18861.01390.1131-0.02870.9065-0.25620.614424.4504198.686650.3108
83.4189-2.93931.35949.2165-1.82922.0917-0.4918-0.6807-0.24030.5588-0.29330.47030.25180.07270.92780.6814-0.00220.24970.7918-0.08990.707516.8771202.313448.0421
96.9197-0.14822.83038.47941.81728.8338-1.36871.05690.29550.02910.6001-1.0579-0.14721.80390.66141.2462-0.39970.11761.3743-0.07211.785847.2175207.547359.7095
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 1:111 ) OR ( CHAIN L AND RESID 1:113 )H1 - 111
2X-RAY DIFFRACTION1( CHAIN H AND RESID 1:111 ) OR ( CHAIN L AND RESID 1:113 )L1 - 113
3X-RAY DIFFRACTION2( CHAIN H AND RESID 112:213 ) OR ( CHAIN L AND RESID 114:211 )H112 - 213
4X-RAY DIFFRACTION2( CHAIN H AND RESID 112:213 ) OR ( CHAIN L AND RESID 114:211 )L114 - 211
5X-RAY DIFFRACTION3( CHAIN F AND RESID 26:73 )F26 - 73
6X-RAY DIFFRACTION4( CHAIN F AND RESID 74:263 )F74 - 263
7X-RAY DIFFRACTION5( CHAIN F AND RESID 264:318 )F264 - 318
8X-RAY DIFFRACTION6( CHAIN F AND RESID 319:363 )F319 - 363
9X-RAY DIFFRACTION7( CHAIN F AND RESID 364:443 )F364 - 443
10X-RAY DIFFRACTION8( CHAIN F AND RESID 444:477 )F444 - 477
11X-RAY DIFFRACTION9( CHAIN F AND RESID 478:513 )F478 - 513

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