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

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Basic information

Entry
Database: PDB / ID: 4mmu
TitleCrystal Structure of Prefusion-stabilized RSV F Variant DS-Cav1 at pH 5.5
Components(Fusion glycoprotein ...) x 2
KeywordsVIRAL PROTEIN / fusion / membrane / structure-based vaccine design
Function / homology
Function and homology information


symbiont-mediated induction of syncytium formation / 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 / virion component / entry receptor-mediated virion attachment to 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 / 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 / virion component / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion 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
PHOSPHATE ION / 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 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 1.1Jul 26, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen / software / Item: _diffrn_detector.detector
Revision 1.2Sep 20, 2017Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jun 2, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.host_org_common_name ..._chem_comp.pdbx_synonyms / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.5Sep 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
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fusion glycoprotein F2
B: Fusion glycoprotein F1 fused with Fibritin trimerization domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5258
Polymers54,8252
Non-polymers7006
Water1,45981
1
A: Fusion glycoprotein F2
B: Fusion glycoprotein F1 fused with Fibritin trimerization domain
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)166,57524
Polymers164,4746
Non-polymers2,10118
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area44620 Å2
ΔGint-457 kcal/mol
Surface area52170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.588, 168.588, 168.588
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

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Fusion glycoprotein ... , 2 types, 2 molecules AB

#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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Sugars , 1 types, 1 molecules

#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.: 1
Source method: isolated from a genetically manipulated source
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 , 3 types, 86 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.64 Å3/Da / Density % sol: 66.22 %
Crystal growpH: 5.5
Details: 1.8 M Ammonium sulphate 0.1 M citrate pH5.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 2, 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→50 Å / Num. obs: 16922 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 16.3 % / Biso Wilson estimate: 74.39 Å2 / Rmerge(I) obs: 0.22 / Rsym value: 0.22 / Net I/σ(I): 22.4

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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→28.5 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.913 / SU R Cruickshank DPI: 0.737 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 859 5.08 %RANDOM
Rwork0.178 ---
obs0.181 16922 99.8 %-
all-16956 --
Displacement parametersBiso mean: 78.06 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: LAST / Resolution: 3→28.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3522 0 39 81 3642
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013607HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.434890HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1275SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes97HARMONIC2
X-RAY DIFFRACTIONt_gen_planes501HARMONIC5
X-RAY DIFFRACTIONt_it3607HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion24.09
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion499SEMIHARMONIC5
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_contact4268SEMIHARMONIC4
LS refinement shellResolution: 3→3.18 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.3027 131 4.94 %
Rwork0.2329 2519 -
all0.2364 2650 -
obs--99.81 %
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)
16.3247-1.9265-1.244904.37642.5659-0.2137-0.9749-0.45790.80380.24310.18010.24020.2716-0.0294-0.13270.07520.024-0.03050.1357-0.1468168.423180.516205.324
21.7017-0.1939-0.73032.55884.0548.42350.23160.4289-0.39260.16610.2842-0.07370.97420.1323-0.51580.11380.0214-0.1541-0.0769-0.0466-0.0347172.573151.832168.77
30-2.5762-2.550202.08485.17720.00440.6884-0.3213-0.2501-0.2434-0.19380.7267-0.04610.239-0.1458-0.1935-0.2155-0.1939-0.2561-0.2592172.03152.954152.737
40.16614.31877.802405.94640-0.00740.9145-0.1187-0.36910.15350.36890.205-0.3768-0.14610.7150.1021-0.08380.0211-0.15550.09188.279163.838171.934
50.15311.7852.18340-0.87682.42160.22560.4232-0.4578-0.85990.07710.17010.44990.8178-0.3027-0.03950.1923-0.1636-0.119-0.1114-0.2117187.352160.199179.797
66.93613.94823.72696.7731-1.4955.6002-0.1935-0.2732-1.1824-0.29070.29810.13951.20420.6824-0.10460.72290.1522-0.1801-0.3851-0.0036-0.0235178.878140.192175.063
71.9068-0.6779-0.15664.21565.21680-0.00060.2834-0.58340.09390.15970.1590.55220.1037-0.15910.3253-0.3301-0.154-0.3252-0.2824-0.116167.441140.976158.727
83.4223.9562.07651.66630.9374.86840.03940.30740.0836-0.3199-0.0011-0.03940.49530.109-0.03830.3724-0.255-0.32160.2018-0.44920.0692161.451141.137144.913
92.2725-2.5931.95110.00331.12550-0.17520.1969-0.09480.28340.22160.5360.5413-0.3465-0.0464-0.1109-0.2207-0.2022-0.2276-0.2529-0.1478165.255153.149160.075
103.9629-2.0658-2.67482.92281.94995.9833-0.3041-0.5081-0.74470.57290.0270.21330.8588-0.14240.27710.1902-0.153-0.2158-0.1792-0.07740.0764170.721154.278178.652
110.55821.20230.75940-0.55763.1089-0.010.1674-0.4127-0.02350.21760.34370.932-0.1708-0.20750.26020.0038-0.1423-0.0075-0.03290.1936174.025156.093182.203
1212.29084.0412-0.08861.40233.40877.1812-0.1329-0.31861.0274-0.44420.13150.6057-0.82050.04960.0015-0.17050.0592-0.0097-0.2018-0.0625-0.2497177.026194.042199.428
134.6389-0.08860.45454.8132-0.27062.308-0.1814-0.09890.22190.17680.02530.21530.2119-0.25390.156-0.14780.03310.0006-0.08740.1276-0.1153178.692172.546199.324
145.3248-1.05512.8165.49966.18280.0434-0.10480.0664-0.0891-0.2505-0.00770.27520.1741-0.12120.1126-0.23450.01780.0248-0.07680.08510.0581182.996192.37197.622
154.466-5.30830.43151.21860.89671.89780.2069-0.07650.13040.2391-0.11520.56010.025-0.0655-0.0917-0.24350.02350.0174-0.0873-0.0349-0.1163165.06192.248195.687
164.78244.1044-1.03262.85753.08570-0.02470.1263-0.2950.18240.07010.5654-0.0717-0.5158-0.0454-0.0630.02580.13420.13840.09750.2545151.462192.567197.363
173.1985-1.35430.82751.6902-0.35844.16350.0145-0.2894-0.20330.08940.15070.41770.3388-0.5513-0.1652-0.06930.0435-0.01990.0173-0.06490.0526160.941190.117195.826
184.0999-4.7582-1.3441.8494-5.42980.6617-0.0994-0.9441-0.60820.42680.39271.22280.2039-0.4859-0.2933-0.1019-0.04150.25280.11130.15930.1505162.733182.393205.468
1917.2265.0510.26662.15741.12261.56230.3555-1.04690.39910.17350.0899-0.1137-0.49430.1664-0.4454-0.11050.0063-0.0572-0.2373-0.0705-0.1912185.938194.636203.264
201.5452-0.17778.539807.67492.81970.0852-0.13610.2180.5052-0.1173-0.8445-0.39730.60130.0321-0.0002-0.2097-0.21920.24950.05540.1818197.232197.739207.539
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|26 - 41}
2X-RAY DIFFRACTION2{A|42 - 75}
3X-RAY DIFFRACTION3{A|76 - 96}
4X-RAY DIFFRACTION4{A|97 - 107}
5X-RAY DIFFRACTION5{B|137 - 162}
6X-RAY DIFFRACTION6{B|163 - 190}
7X-RAY DIFFRACTION7{B|191 - 205}
8X-RAY DIFFRACTION8{B|206 - 218}
9X-RAY DIFFRACTION9{B|219 - 236}
10X-RAY DIFFRACTION10{B|237 - 270}
11X-RAY DIFFRACTION11{B|271 - 314}
12X-RAY DIFFRACTION12{B|315 - 338}
13X-RAY DIFFRACTION13{B|339 - 392}
14X-RAY DIFFRACTION14{B|393 - 401}
15X-RAY DIFFRACTION15{B|402 - 426}
16X-RAY DIFFRACTION16{B|427 - 434}
17X-RAY DIFFRACTION17{B|435 - 459}
18X-RAY DIFFRACTION18{B|460 - 472}
19X-RAY DIFFRACTION19{B|473 - 493}
20X-RAY DIFFRACTION20{B|494 - 509}

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