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- PDB-6dc5: RSV prefusion F in complex with AM22 Fab -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6dc5
TitleRSV prefusion F in complex with AM22 Fab
Components
  • Fab AM22 heavy chain
  • Fab AM22 light chain
  • RSV fusion glycoprotein
KeywordsIMMUNE SYSTEM / Viral fusion glycoprotein / human antibody
Function / homology
Function and homology information


positive regulation of syncytium formation by virus / host cell Golgi membrane / immunoglobulin complex / 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 / extracellular region ...positive regulation of syncytium formation by virus / host cell Golgi membrane / immunoglobulin complex / 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 / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Fibritin C-terminal / Fibritin C-terminal region / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulins and major histocompatibility complex proteins signature. ...Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Fibritin C-terminal / Fibritin C-terminal region / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / Envelope glycoprotein / Fusion glycoprotein F0 / IGH@ protein / Ig-like domain-containing protein
Similarity search - Component
Biological speciesHuman respiratory syncytial virus A
Human immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsJones, H.G. / McLellan, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM113132 United States
CitationJournal: Plos Pathog. / Year: 2019
Title: Alternative conformations of a major antigenic site on RSV F.
Authors: Jones, H.G. / Battles, M.B. / Lin, C.C. / Bianchi, S. / Corti, D. / McLellan, J.S.
History
DepositionMay 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 22, 2020Group: 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 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / 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_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: RSV fusion glycoprotein
D: RSV fusion glycoprotein
G: RSV fusion glycoprotein
B: Fab AM22 heavy chain
C: Fab AM22 light chain
E: Fab AM22 heavy chain
F: Fab AM22 light chain
H: Fab AM22 heavy chain
I: Fab AM22 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)333,48421
Polymers331,8469
Non-polymers1,63812
Water0
1
A: RSV fusion glycoprotein
B: Fab AM22 heavy chain
C: Fab AM22 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,1617
Polymers110,6153
Non-polymers5464
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: RSV fusion glycoprotein
E: Fab AM22 heavy chain
F: Fab AM22 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,1617
Polymers110,6153
Non-polymers5464
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: RSV fusion glycoprotein
H: Fab AM22 heavy chain
I: Fab AM22 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,1617
Polymers110,6153
Non-polymers5464
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.450, 152.180, 202.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

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Antibody , 2 types, 6 molecules BEHCFI

#2: Antibody Fab AM22 heavy chain


Mass: 24123.217 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGH@ / Production host: Homo sapiens (human) / References: UniProt: Q6GMX6
#3: Antibody Fab AM22 light chain


Mass: 23273.938 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: Q8TCD0

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Protein / Sugars , 2 types, 6 molecules ADG

#1: Protein RSV fusion glycoprotein / Protein F


Mass: 63218.344 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A (strain A2), (gene. exp.) Human immunodeficiency virus 1
Strain: A2 / Production host: Homo sapiens (human) / References: UniProt: P03420, UniProt: M1E1E4
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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 , 2 types, 9 molecules

#5: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3

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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: 3.08 Å3/Da / Density % sol: 60.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 32% PEG 400, 4% PEG 3350, 0.01 M cadmium chloride, 0.1 M sodium acetate pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→50.55 Å / Num. obs: 52333 / % possible obs: 99.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 58.62 Å2 / CC1/2: 0.933 / Net I/σ(I): 5.7
Reflection shellResolution: 3.5→3.61 Å / Rmerge(I) obs: 0.903 / Mean I/σ(I) obs: 2 / Num. unique obs: 4425 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MMS, 6DC4

4mms

6dc4


Resolution: 3.5→47.231 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / Phase error: 24.93
RfactorNum. reflection% reflection
Rfree0.2801 2606 4.98 %
Rwork0.2172 --
obs-52294 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 211.52 Å2 / Biso min: 3.96 Å2
Refinement stepCycle: final / Resolution: 3.5→47.231 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20199 0 86 0 20285
Biso mean--40.7 --
Num. residues----2644
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.56360.3171530.2992532X-RAY DIFFRACTION98
3.5636-3.63220.36051260.28862543X-RAY DIFFRACTION99
3.6322-3.70630.36371360.29252586X-RAY DIFFRACTION99
3.7063-3.78680.38021190.29152601X-RAY DIFFRACTION100
3.7868-3.87490.36251130.26852589X-RAY DIFFRACTION100
3.8749-3.97170.30361560.26282600X-RAY DIFFRACTION100
3.9717-4.07910.31421390.25322548X-RAY DIFFRACTION100
4.0791-4.1990.29791550.2282602X-RAY DIFFRACTION100
4.199-4.33450.28531360.21842591X-RAY DIFFRACTION100
4.3345-4.48930.26311520.20942591X-RAY DIFFRACTION100
4.4893-4.66890.27081340.19542585X-RAY DIFFRACTION100
4.6689-4.88110.23881370.18132616X-RAY DIFFRACTION100
4.8811-5.13820.24811340.18432618X-RAY DIFFRACTION100
5.1382-5.45970.23481440.19532638X-RAY DIFFRACTION100
5.4597-5.88050.22061150.19932638X-RAY DIFFRACTION100
5.8805-6.47090.26781370.18772635X-RAY DIFFRACTION100
6.4709-7.40420.26661440.19982659X-RAY DIFFRACTION100
7.4042-9.31680.23651260.16142712X-RAY DIFFRACTION100
9.3168-47.230.24031500.17662804X-RAY DIFFRACTION100
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)
12.03271.0555-0.00781.504-0.19070.0377-0.0589-0.33250.52220.10860.0982-0.3363-0.47890.1566-0.00461.3415-0.0815-0.00220.4216-0.21190.8597-45.774496.388-47.695
26.3266-1.5976-0.49274.62321.39112.2575-0.3341-0.20760.0913-0.34310.2863-0.0906-0.4821-0.06280.0110.6358-0.0180.22451.04110.05030.4566-65.528449.2481-33.731
32.13672.66620.61364.5628-1.22093.3668-0.029-0.1269-0.19210.4207-0.00980.5908-0.4626-0.09650.05310.27420.08770.14740.46110.05680.3332-61.013860.1463-33.4903
40.2983-0.66360.08783.96140.17580.65290.0022-0.15730.0961-0.72350.12550.5079-0.477-0.3718-0.05990.50980.20330.07770.37920.04140.5411-62.750569.3234-45.3252
51.22040.7741-0.08562.85810.07560.8327-0.1427-0.16460.4808-0.13070.1912-0.1222-0.43960.1098-0.03470.94680.186-0.01310.2289-0.21550.5184-49.537291.4059-44.4553
60.24170.13840.07840.1398-0.03370.1194-0.0809-0.27850.7194-0.03840.0977-0.2187-0.6686-0.0756-0.07411.6998-0.0019-0.23450.4738-0.34891.5062-35.6084111.7512-36.9838
72.04430.5763-0.64050.406-0.26840.43470.0720.27990.2142-0.08920.27580.5230.0045-0.4089-0.01730.0995-0.11840.00060.61030.39360.8115-81.730330.6306-43.3663
82.51680.59640.56451.06340.47072.46810.0712-0.248-0.05170.19650.01410.0450.2118-0.179-0.04150.0596-0.05250.04280.29990.08520.5609-85.9045-0.5577-23.8962
91.36740.6159-0.69371.012-0.1370.73160.06110.116-0.0335-0.17170.2298-0.044-0.0069-0.1461-0.0360.057-0.12860.02520.38120.19980.372-61.710924.0698-40.245
102.1040.48080.68511.47760.62261.40450.05780.4527-0.28120.00420.0972-0.0585-0.0070.1557-0.12280.08680.03870.03740.39670.05620.5208-75.0568-6.9288-34.4131
115.7758-0.3977-2.55090.1171-0.07925.5863-0.1735-0.36380.8772-0.0135-0.07350.6581-0.5805-0.14780.22640.99480.4387-0.10180.7049-0.25740.7707-74.9712102.5069-29.7472
120.78050.0985-0.30451.36730.07880.1225-0.3791-0.3925-0.01140.20980.1444-0.2662-0.6258-0.35660.17850.84110.5385-0.07461.072-0.00160.5171-52.639472.2963-16.2443
134.4423-0.52720.49924.8465-1.07883.22090.1733-0.20490.05680.22680.2111-0.1869-0.4302-0.0392-0.35280.15820.06510.06450.337-0.05990.2657-33.708256.724-26.0336
140.2279-0.0643-0.15981.68371.20910.9136-0.2104-0.2945-0.04870.2487-0.10640.4447-0.3171-0.42570.13020.98080.46460.31531.2161-0.09840.543-49.1868.8628-9.6961
150.4555-0.24830.32010.159-0.170.224-0.4616-0.77570.37670.20740.3040.0085-0.6108-0.4464-0.00760.9970.69260.05141.0014-0.3450.6747-60.851888.9432-27.3512
161.83520.37410.92840.3356-0.54592.551-0.1050.0885-0.1888-0.1857-0.1777-0.52450.10530.21180.23731.66020.5118-0.42651.1721-0.71162.0852-59.9691126.8799-21.6761
172.3684-1.13151.25721.5005-1.05841.7638-0.2167-0.40230.04580.28850.22090.0983-0.0280.03940.01180.17480.08510.05960.52580.14380.2558-24.266325.347-13.1357
184.3895-0.0392-0.32882.7886-0.31592.4705-0.07210.056-0.12550.05230.1719-0.3136-0.00870.0872-0.02040.2320.1694-0.04560.52480.12810.33771.97143.527-27.6937
191.6318-0.741-0.20581.7630.27991.46840.042-0.5951-0.122-0.11970.10610.08630.1136-0.068-0.09610.1425-0.0082-0.06530.3630.15350.3146-29.93423.8073-33.5071
200.9283-1.47710.96033.1704-2.26843.09410.2331-0.113-0.2055-0.12590.07080.54010.1859-0.2344-0.27430.17090.0073-0.05190.4870.0580.5286-11.5762-3.7073-33.9361
210.23030.1226-0.0970.08230.02850.2293-0.1696-0.53280.33910.51790.10940.2677-0.4271-0.2528-0.03731.17830.33750.05590.88-0.57790.9544-31.652490.0116-18.607
221.8-2.4666-1.9276.7462-1.76619.6046-0.3649-0.33931.32720.4519-0.1694-0.0217-1.05150.15060.4940.7670.0065-0.07670.5371-0.05790.5998-38.384259.1849-60.4465
233.5495-0.6210.04941.59320.63282.0039-0.12720.20380.3583-0.40160.2710.7056-0.6173-0.3029-0.06360.34150.0388-0.02070.24590.12430.3642-41.491863.7637-51.5952
240.27830.47380.31391.15860.18350.6127-0.058-0.12950.15410.00560.0202-0.5498-0.60590.2441-0.09840.5661-0.17290.13060.3335-0.28791.0196-25.412175.9387-44.4305
250.8438-0.2379-0.13982.7030.77660.685-0.1772-0.74420.39650.39640.2846-0.6015-0.42030.0298-0.20480.5920.1319-0.0450.5646-0.3110.7657-31.986176.3465-32.4169
260.3965-0.1635-0.1450.15430.23690.3799-0.1141-0.24210.4757-0.11520.00330.0328-0.4082-0.2322-0.14151.51940.6954-0.33831.4547-0.94341.0657-44.5262104.3638-8.4211
270.1013-0.1634-0.18110.33160.15110.8563-0.08090.08420.1109-0.27330.1898-0.4457-0.31180.3596-0.14370.4329-0.34530.22150.3444-0.12380.3617-26.575640.8971-76.131
285.27250.0088-0.55183.56150.19243.1260.28010.37420.1338-0.78410.020.1903-0.56330.259-0.23120.5513-0.0832-0.08370.26540.01710.2918-45.303218.354-99.7443
291.81480.31920.22552.14620.10252.21420.149-0.0138-0.06150.2884-0.06870.0842-0.15450.2383-0.09590.151-0.11690.00910.17160.04030.2572-40.228531.0464-63.4771
302.8358-0.4915-1.25482.03471.05372.41120.1743-0.0855-0.3186-0.1318-0.0334-0.0777-0.0960.0232-0.13720.1348-0.0999-0.10050.28450.02520.2275-41.96458.0595-87.4931
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 27:62)A27 - 62
2X-RAY DIFFRACTION2(chain A and resid 63:73)A63 - 73
3X-RAY DIFFRACTION3(chain A and resid 74:98)A74 - 98
4X-RAY DIFFRACTION4(chain A and resid 137:234)A137 - 234
5X-RAY DIFFRACTION5(chain A and resid 235:348)A235 - 348
6X-RAY DIFFRACTION6(chain A and resid 349:509)A349 - 509
7X-RAY DIFFRACTION7(chain B and resid 1:111)B1 - 111
8X-RAY DIFFRACTION8(chain B and resid 112:215)B112 - 215
9X-RAY DIFFRACTION9(chain C and resid 1:105)C1 - 105
10X-RAY DIFFRACTION10(chain C and resid 106:212)C106 - 212
11X-RAY DIFFRACTION11(chain D and resid 26:41)D26 - 41
12X-RAY DIFFRACTION12(chain D and resid 42:67)D42 - 67
13X-RAY DIFFRACTION13(chain D and resid 68:98)D68 - 98
14X-RAY DIFFRACTION14(chain D and resid 137:202)D137 - 202
15X-RAY DIFFRACTION15(chain D and resid 203:475)D203 - 475
16X-RAY DIFFRACTION16(chain D and resid 476:511)D476 - 511
17X-RAY DIFFRACTION17(chain E and resid 1:111)E1 - 111
18X-RAY DIFFRACTION18(chain E and resid 112:215)E112 - 215
19X-RAY DIFFRACTION19(chain F and resid 1:105)F1 - 105
20X-RAY DIFFRACTION20(chain F and resid 106:211)F106 - 211
21X-RAY DIFFRACTION21(chain G and resid 27:62)G27 - 62
22X-RAY DIFFRACTION22(chain G and resid 63:71)G63 - 71
23X-RAY DIFFRACTION23(chain G and resid 72:97)G72 - 97
24X-RAY DIFFRACTION24(chain G and resid 137:210)G137 - 210
25X-RAY DIFFRACTION25(chain G and resid 211:322)G211 - 322
26X-RAY DIFFRACTION26(chain G and resid 323:509)G323 - 509
27X-RAY DIFFRACTION27(chain H and resid 1:111)H1 - 111
28X-RAY DIFFRACTION28(chain H and resid 112:216)H112 - 216
29X-RAY DIFFRACTION29(chain I and resid 1:105)I1 - 105
30X-RAY DIFFRACTION30(chain I and resid 106:214)I106 - 214

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Yorodumi

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  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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