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- PDB-4mmt: Crystal Structure of Prefusion-stabilized RSV F Variant DS-Cav1 a... -

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Basic information

Entry
Database: PDB / ID: 4mmt
TitleCrystal Structure of Prefusion-stabilized RSV F Variant DS-Cav1 at pH 9.5
Components
  • Fusion glycoprotein F1 fused with Fibritin trimerization domain
  • Fusion glycoprotein F2
KeywordsVIRAL PROTEIN / fusion / membrane / structure-based vaccine design
Function / homology
Function and homology information


positive regulation of syncytium formation by virus / host cell Golgi membrane / virion component / 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
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
Similarity search - Component
Biological speciesHuman respiratory syncytial virus A2
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsJoyce, M.G. / Mclellan, J.S. / Stewart-Jones, G.B.E. / Sastry, M. / Yang, Y. / Graham, B.S. / Kwong, P.D.
CitationJournal: Science / Year: 2013
Title: Structure-based design of a fusion glycoprotein vaccine for respiratory syncytial virus.
Authors: McLellan, J.S. / Chen, M. / Joyce, M.G. / Sastry, M. / Stewart-Jones, G.B. / Yang, Y. / Zhang, B. / Chen, L. / Srivatsan, S. / Zheng, A. / Zhou, T. / Graepel, K.W. / Kumar, A. / Moin, S. / ...Authors: McLellan, J.S. / Chen, M. / Joyce, M.G. / Sastry, M. / Stewart-Jones, G.B. / Yang, Y. / Zhang, B. / Chen, L. / Srivatsan, S. / Zheng, A. / Zhou, T. / Graepel, K.W. / Kumar, A. / Moin, S. / Boyington, J.C. / Chuang, G.Y. / Soto, C. / Baxa, U. / Bakker, A.Q. / Spits, H. / Beaumont, T. / Zheng, Z. / Xia, N. / Ko, S.Y. / Todd, J.P. / Rao, S. / Graham, B.S. / Kwong, P.D.
History
DepositionSep 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Jul 26, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen / software / Item: _diffrn_detector.detector
Revision 1.3Jun 2, 2021Group: Database references / Source and taxonomy / Category: entity_src_gen / struct_ref_seq_dif
Item: _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line ..._entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _struct_ref_seq_dif.details
Revision 1.4Sep 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
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 F2
B: Fusion glycoprotein F1 fused with Fibritin trimerization domain


Theoretical massNumber of molelcules
Total (without water)54,8252
Polymers54,8252
Non-polymers00
Water0
1
A: Fusion glycoprotein F2
B: Fusion glycoprotein F1 fused with Fibritin trimerization domain

A: Fusion glycoprotein F2
B: Fusion glycoprotein F1 fused with Fibritin trimerization domain

A: Fusion glycoprotein F2
B: Fusion glycoprotein F1 fused with Fibritin trimerization domain


Theoretical massNumber of molelcules
Total (without water)164,4746
Polymers164,4746
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area36060 Å2
ΔGint-237 kcal/mol
Surface area54930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.726, 170.726, 170.726
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein Fusion glycoprotein F2


Mass: 9215.410 Da / Num. of mol.: 1 / Mutation: P102A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A2 / Gene: F / Plasmid: p(alpha)H / Cell line (production host): FreeStyle(tm) 293-F / Production host: Homo sapiens (human) / References: UniProt: P03420
#2: Protein Fusion glycoprotein F1 fused with Fibritin trimerization domain


Mass: 45609.148 Da / Num. of mol.: 1 / Mutation: S155C, S190F, V207L, S290C, I379V, M447V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A2, (gene. exp.) Enterobacteria phage T4 (virus)
Gene: F / Plasmid: p(alpha)H / Cell line (production host): FreeStyle(tm) 293-F / Production host: Homo sapiens (human) / References: UniProt: P03420, UniProt: P10104

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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: 3.78 Å3/Da / Density % sol: 67.48 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 9.5
Details: 1.8 M Na/K tartrate, 0.2 M LiSO4, 0.1 M CHES pH9.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 19, 2013 / Details: Si 111
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. all: 16772 / Num. obs: 16252 / % possible obs: 96.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Biso Wilson estimate: 88.15 Å2 / Rmerge(I) obs: 0.14 / Rsym value: 0.14 / Net I/σ(I): 11.4

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
BUSTER2.10.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4JHW

4jhw


Resolution: 3.05→45.63 Å / Cor.coef. Fo:Fc: 0.9267 / Cor.coef. Fo:Fc free: 0.9283 / SU R Cruickshank DPI: 0.79 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2432 816 5.04 %RANDOM
Rwork0.2306 ---
obs0.2312 16192 96.56 %-
all-16762 --
Displacement parametersBiso mean: 104.47 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.801 Å
Refinement stepCycle: LAST / Resolution: 3.05→45.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3510 0 0 0 3510
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083567HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.074836HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1264SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes97HARMONIC2
X-RAY DIFFRACTIONt_gen_planes497HARMONIC5
X-RAY DIFFRACTIONt_it3567HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.9
X-RAY DIFFRACTIONt_other_torsion24.3
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion498SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4068SEMIHARMONIC4
LS refinement shellResolution: 3.05→3.26 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3018 146 5.13 %
Rwork0.2658 2699 -
all0.2677 2845 -
obs--96.56 %
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)
11.8308-2.1286-1.19070.5391-1.54022.7063-0.0078-0.0559-0.16520.01340.00440.09490.3225-0.10080.00340.1195-0.0190.06190.09030.06920.0251-4.93695.710936.0814
20.7645-0.0010.25350.48821.93912.963-0.0029-0.00470.02110.02870.0334-0.08060.03010.0967-0.03050.16290.0766-0.1272-0.0282-0.2541-0.10373.198819.373639.2679
31.5387-0.0414-1.87520.0219-1.89032.4757-0.01550.0124-0.01660.0037-0.01960.06350.3214-0.15230.0352-0.00980.0378-0.0201-0.07740.1157-0.17211.899111.078635.2672
44.2555-1.7701-0.41521.9945-3.21100.1336-0.1247-0.35660.1162-0.03270.32750.29240.0132-0.1009-0.1177-0.1042-0.0595-0.16120.0675-0.19378.4393-8.730822.176
52.4038-1.41020.73841.19393.885700.01870.37740.0141-0.1629-0.0495-0.16350.13310.05630.03080.1947-0.0907-0.2519-0.3714-0.1549-0.03898.2391-23.3511-6.4352
60.4036-0.394-0.87281.25190.9790.77810.00390.0082-0.0111-0.002-0.0251-0.0238-0.0118-0.01440.02120.19320.002-0.1520.2196-0.06910.2281.485-23.6059-25.7088
70.46860.17360.07360.29560.18880.1952-0.00350.03960.011-0.010.0111-0.0084-0.0104-0.0099-0.00770.1215-0.00410.03150.2124-0.10010.1741-11.0783-22.4851-23.5806
800.19390.695900.38950.15980.01330.03610.0495-0.0198-0.0185-0.0515-0.01930.00570.00520.0582-0.1294-0.2992-0.027-0.2969-0.2737-5.5398-17.5889-18.4377
90-0.00651.28940.00110.330300.00420.06440.037-0.0505-0.0108-0.0627-0.00740.05410.00660.1197-0.3136-0.2858-0.0457-0.2694-0.32462.494-17.0117-15.0453
1001.7565-3.58992.9284-0.62031.2821-0.0001-0.0369-0.0281-0.03540.0128-0.1810.01440.1056-0.01270.21850.0128-0.1932-0.0623-0.2174-0.208713.0256-11.6324-9.6428
113.2283-0.55350.56361.11150.28633.59290.06070.3158-0.399-0.21620.12150.16910.1850.1094-0.1822-0.0819-0.0172-0.0611-0.1612-0.0057-0.255919.6679-5.0513.0835
120.4257-0.28570.00321.86210.4140.8756-0.0030.0177-0.0018-0.0445-0.0246-0.0898-0.03060.08910.02760.38590.29060.0246-0.1657-0.20090.370320.1625-27.32451.3544
130.0615-6.0819-3.89395.9459-4.01385.451-0.0104-0.0887-0.1972-0.1023-0.1666-0.0690.1610.39860.1770.2913-0.2041-0.2501-0.37030.1240.256713.2597-28.04997.9598
141.47843.40692.192100.66170.11550.01390.0692-0.1613-0.0762-0.0478-0.00270.07210.04140.0339-0.0058-0.3344-0.3904-0.4349-0.4131-0.01612.0683-26.5506-4.5985
150.84550.3533-0.51650.38211.19760.29030.01190.0631-0.0082-0.0799-0.0153-0.04210.01230.00070.00340.1707-0.2024-0.0580.1032-0.09260.1979-2.4618-31.1624-20.4705
164.4526-2.3217-0.13812.8713-0.64680.45250.00990.1342-0.0079-0.03330.00720.07250.05030.004-0.0170.1386-0.08160.08050.1057-0.25150.0689-9.9773-24.5106-14.0364
170.00432.72960.69880-1.8580.8571-0.00040.0431-0.01040.0090.0250.1974-0.1087-0.1086-0.0246-0.0089-0.1645-0.2164-0.1099-0.2159-0.06410.3998-13.2774-4.3271
184.13892.0691-0.81053.74761.06871.55030.02380.0238-0.87880.096-0.22740.28290.3426-0.30970.20360.0542-0.1833-0.2085-0.2213-0.02650.10383.5823-14.001710.6519
190.4954-0.4725-2.12880.43072.63540.71320.02640.00510.10430.15560.020.1470.0108-0.1404-0.04650.0038-0.3001-0.0647-0.08460.00710.2716-1.4017-12.64821.2571
206.9641-0.0594-1.74091.082-2.15860.02110.04980.52-0.4056-0.61690.0011-0.04790.57230.2695-0.05090.207-0.0875-0.1225-0.1139-0.0774-0.01349.8665-13.88034.0034
212.1657-1.4219-0.43210.86090.53231.8604-0.0473-0.14920.04620.02120.07930.35910.0679-0.2825-0.032-0.0704-0.0511-0.0069-0.1189-0.062-0.12016.92727.395427.8808
223.1312-1.27741.12410.40723.87675.95640.0188-0.16370.6588-0.04650.0581-0.0329-0.50340.1433-0.07690.0120.0243-0.0628-0.0881-0.0739-0.072610.603122.14430.5613
231.8672-1.38660.1143.1490.25670.3748-0.0342-0.41020.10190.19770.042-0.00350.1201-0.238-0.0078-0.0211-0.0041-0.0414-0.0595-0.0131-0.07868.07211.730530.7065
241.324-1.68890.742400.998600.04120.2215-0.1155-0.1880.03960.27370.1205-0.3113-0.0809-0.03470.02290.11410.262-0.210.2795-17.542523.876527.5367
251.22880.9108-0.52513.0309-0.40192.7090.0604-0.4120.15840.4408-0.09160.10780.0461-0.45220.0313-0.11490.10030.04050.0332-0.13350.1344-6.977923.388228.749
264.4012-4.37051.21010-1.53669.74820.0058-0.5044-0.03890.05880.01920.49940.1911-0.1343-0.0250.04410.01090.1544-0.0467-0.0344-0.0211-6.10615.345733.541
273.27550.4034-0.11352.6608-1.28754.85720.0083-0.20580.58420.0857-0.2363-0.3303-0.23770.02650.2280.05780.0234-0.1422-0.1452-0.16720.128916.943228.818836.3367
280.508-1.47711.35172.847-1.50030.7884-0.0163-0.02080.0840.0656-0.0639-0.14010.0240.17170.0801-0.2413-0.0306-0.2039-0.1952-0.1336-0.104624.918224.223838.4853
290.5842-0.61441.15250.72610.12261.34240.0067-0.0109-0.03780.00030.01060.0466-0.00330.031-0.01730.1545-0.1721-0.07680.2060.05230.181734.672940.253645.4908
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|26 - 31}A26 - 31
2X-RAY DIFFRACTION2{A|32 - 36}A32 - 36
3X-RAY DIFFRACTION3{A|37 - 43}A37 - 43
4X-RAY DIFFRACTION4{A|44 - 55}A44 - 55
5X-RAY DIFFRACTION5{A|56 - 65}A56 - 65
6X-RAY DIFFRACTION6{A|66 - 70}A66 - 70
7X-RAY DIFFRACTION7{A|71 - 76}A71 - 76
8X-RAY DIFFRACTION8{A|77 - 82}A77 - 82
9X-RAY DIFFRACTION9{A|83 - 87}A83 - 87
10X-RAY DIFFRACTION10{A|88 - 98}A88 - 98
11X-RAY DIFFRACTION11{B|137 - 160}B137 - 160
12X-RAY DIFFRACTION12{B|161 - 167}B161 - 167
13X-RAY DIFFRACTION13{B|168 - 189}B168 - 189
14X-RAY DIFFRACTION14{B|190 - 201}B190 - 201
15X-RAY DIFFRACTION15{B|202 - 211}B202 - 211
16X-RAY DIFFRACTION16{B|212 - 224}B212 - 224
17X-RAY DIFFRACTION17{B|225 - 236}B225 - 236
18X-RAY DIFFRACTION18{B|237 - 269}B237 - 269
19X-RAY DIFFRACTION19{B|270 - 279}B270 - 279
20X-RAY DIFFRACTION20{B|280 - 299}B280 - 299
21X-RAY DIFFRACTION21{B|300 - 327}B300 - 327
22X-RAY DIFFRACTION22{B|328 - 341}B328 - 341
23X-RAY DIFFRACTION23{B|342 - 424}B342 - 424
24X-RAY DIFFRACTION24{B|425 - 433}B425 - 433
25X-RAY DIFFRACTION25{B|434 - 456}B434 - 456
26X-RAY DIFFRACTION26{B|457 - 472}B457 - 472
27X-RAY DIFFRACTION27{B|473 - 488}B473 - 488
28X-RAY DIFFRACTION28{B|489 - 504}B489 - 504
29X-RAY DIFFRACTION29{B|505 - 516}B505 - 516

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