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- PDB-6apb: Crystal Structure of Non-Neutralizing Infant Antibody ADI-14359 i... -

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Basic information

Entry
Database: PDB / ID: 6apb
TitleCrystal Structure of Non-Neutralizing Infant Antibody ADI-14359 in Complex with Postfusion RSV F Glycoprotein
Components
  • ADI-14359 Fab Light Chain
  • Fusion glycoprotein F0,Fusion glycoprotein F0
  • IgG H chain
KeywordsIMMUNE SYSTEM / viral fusion glycoprotein / immunoglobulin / respiratory syncytial virus
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 / membrane => GO:0016020 / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane ...positive regulation of syncytium formation by virus / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / membrane => GO:0016020 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fusion glycoprotein F0 / Fusion glycoprotein F0 / Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respiratory syncytial virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGilman, M.S.A. / McLellan, J.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008704 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103393 United States
CitationJournal: Immunity / Year: 2018
Title: Infants Infected with Respiratory Syncytial Virus Generate Potent Neutralizing Antibodies that Lack Somatic Hypermutation.
Authors: Goodwin, E. / Gilman, M.S.A. / Wrapp, D. / Chen, M. / Ngwuta, J.O. / Moin, S.M. / Bai, P. / Sivasubramanian, A. / Connor, R.I. / Wright, P.F. / Graham, B.S. / McLellan, J.S. / Walker, L.M.
History
DepositionAug 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jul 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 1.3Oct 4, 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: Fusion glycoprotein F0,Fusion glycoprotein F0
B: Fusion glycoprotein F0,Fusion glycoprotein F0
C: Fusion glycoprotein F0,Fusion glycoprotein F0
H: IgG H chain
L: ADI-14359 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,0448
Polymers218,3805
Non-polymers6643
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38540 Å2
ΔGint-237 kcal/mol
Surface area70420 Å2
Unit cell
Length a, b, c (Å)88.450, 99.040, 323.309
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid
21chain B and segid
31chain C and segid

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segidA0
211chain B and segidB0
311chain C and segidC0

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Components

#1: Protein Fusion glycoprotein F0,Fusion glycoprotein F0


Mass: 56758.934 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus / Gene: F, MZ07_64039gpF, MZ07_64040gpF / Cell line (production host): FreeStyle 293-F / Production host: Homo sapiens (human)
References: UniProt: Q84850, UniProt: A0A1P8J9V4, UniProt: P03420*PLUS
#2: Antibody IgG H chain


Mass: 24824.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): FreeStyle 293-F / Production host: Homo sapiens (human)
#3: Antibody ADI-14359 Fab Light Chain


Mass: 23278.748 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): FreeStyle 293-F / Production host: Homo sapiens (human)
#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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.53 Å3/Da / Density % sol: 65.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 4.45mg/mL ADI-14359 Fab-postF complex, 13% PEG8000, 0.43M Ammonium Citrate pH 8.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.1809 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1809 Å / Relative weight: 1
ReflectionResolution: 3→51.11 Å / Num. obs: 57978 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 35.31 Å2 / CC1/2: 0.952 / Rmerge(I) obs: 0.449 / Rpim(I) all: 0.177 / Rrim(I) all: 0.483 / Net I/σ(I): 5.2 / Num. measured all: 423092 / Scaling rejects: 1081
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3-3.087.41.6623276944390.5640.651.7861.6100
13.08-51.116.30.09550988100.9940.040.10310.598.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLM7.1.0data reduction
Aimless0.5.28data scaling
PDB_EXTRACT3.22data extraction
Coot0.8.6.1model building
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RRT, 3QHZ, 4KMT

3rrt

3qhz

4kmt


Resolution: 3→51.108 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2547 2880 4.98 %
Rwork0.2217 54941 -
obs0.2233 57821 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.53 Å2 / Biso mean: 37.8749 Å2 / Biso min: 14.55 Å2
Refinement stepCycle: final / Resolution: 3→51.108 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13264 0 42 0 13306
Biso mean--62.63 --
Num. residues----1713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413548
X-RAY DIFFRACTIONf_angle_d0.86318349
X-RAY DIFFRACTIONf_chiral_restr0.0382206
X-RAY DIFFRACTIONf_plane_restr0.0042300
X-RAY DIFFRACTIONf_dihedral_angle_d12.7194961
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6076X-RAY DIFFRACTION7.046TORSIONAL
12B6076X-RAY DIFFRACTION7.046TORSIONAL
13C6076X-RAY DIFFRACTION7.046TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3-3.04920.41031420.35325822724
3.0492-3.10180.38071450.33625662711
3.1018-3.15820.33321300.319225712701
3.1582-3.21890.35231370.303725732710
3.2189-3.28460.34681390.29425882727
3.2846-3.3560.31711230.277225532676
3.356-3.4340.32941250.282126142739
3.434-3.51990.29381520.257525582710
3.5199-3.6150.31921480.246125822730
3.615-3.72140.31271320.26526012733
3.7214-3.84150.25891210.234326312752
3.8415-3.97870.28571300.241225882718
3.9787-4.1380.25541430.186226152758
4.138-4.32620.19551160.17326082724
4.3262-4.55410.18971500.161425932743
4.5541-4.83930.16721600.154426112771
4.8393-5.21260.21751650.160726222787
5.2126-5.73650.18621150.183626552770
5.7365-6.56510.21511280.191926852813
6.5651-8.26570.19891320.181127202852
8.2657-51.11570.16341470.165828252972
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)
10.8225-0.0404-0.24041.3097-0.57311.528-0.12430.41370.0623-0.2030.11020.1784-0.31550.26660.02820.11430.00830.01020.26170.0060.28736.85357.946-12.3762
20.3939-0.028-0.6480.21530.39962.26080.05770.1180.0488-0.05660.0309-0.0038-0.0033-0.1098-0.0940.26910.0493-0.00970.18650.00620.199215.94446.6319-30.7812
38.0479-2.2115-2.44214.0875-2.34356.77250.01270.1526-0.3699-0.1536-0.14530.15930.18590.02580.05740.326-0.0131-0.04410.18610.03750.22927.676214.228315.5445
41.3877-0.0948-1.15721.24040.20874.80560.0521-0.29790.01670.32810.0303-0.29670.16210.5952-0.05530.3403-0.0231-0.00680.25890.01170.280424.13980.002820.2571
53.22430.2249-1.25371.9092-1.43432.34090.0944-0.1469-0.0648-0.0882-0.07730.0812-1.28921.4322-0.10550.7201-0.04720.02530.2929-0.02210.288238.53326.1912-75.9181
61.45860.0316-0.64471.11030.39651.61250.10560.5243-0.0114-0.253-0.16270.0116-0.1669-0.17560.07860.19530.0213-0.0720.19920.1150.2125.0596-6.6212-12.4876
70.67130.0296-0.95470.1775-0.0111.9018-0.09070.1116-0.0624-0.06160.00890.014-0.0095-0.06490.05920.26210.0037-0.04090.23010.03580.184411.0788-4.7044-32.7229
84.0426-0.1092-0.29978.0845-1.48717.5721-0.1224-0.08120.3202-0.366-0.0327-0.7653-0.557-0.03070.11730.2942-0.0063-0.00240.2287-0.07650.2785-11.6441-0.98439.5039
91.269-0.2011-1.52870.86250.54343.17260.11630.06750.1760.14030.04910.1314-0.4067-0.2591-0.17710.35550.0935-0.02510.2685-0.01320.3174-8.019620.952210.104
102.12820.3685-2.51831.3786-0.4675.54150.13940.6837-0.0197-0.3298-0.40580.0934-0.7693-2.26840.25370.45630.0896-0.15490.5817-0.0140.30622.3835-0.2768-83.1031
111.04790.04210.14210.52560.10780.19430.07910.09410.1292-0.2241-0.1124-0.0778-0.12150.24320.02070.3210.02130.00150.13-0.03580.235517.9532-1.0816-8.5444
120.1484-0.0298-0.62110.2203-0.06992.03780.00490.1237-0.0127-0.11490.01480.0341-0.1477-0.2145-0.01650.2773-0.0483-0.03360.2705-0.0450.180722.9531-3.1603-28.9117
134.8830.8007-1.57923.62450.6643.96450.06780.16960.27780.3637-0.17680.1906-0.2574-0.18540.10270.22080.0227-0.00570.240.02090.18057.6635-11.488321.1517
141.52860.60580.12731.1468-0.51440.4978-0.12470.056-0.0321-0.0324-0.03610.20410.1621-0.25070.14530.1982-0.0163-0.03150.18980.00480.2454-10.1748-19.09723.8831
158.21890.1464-6.77621.8681-0.15137.0114-0.6944-0.1438-0.5771-0.0682-0.20190.05770.69110.55310.74780.5275-0.0546-0.03880.40360.0030.207236.3248-12.0306-78.378
161.0863-0.68190.41691.9947-1.00611.56490.0554-0.10510.13110.1669-0.0897-0.1846-0.15790.10770.0210.3724-0.0309-0.050.2204-0.00440.2038.1996-31.805550.1452
174.34341.0092-1.1573.50290.46736.118-0.0514-0.0215-0.14690.08490.342-0.64530.23390.3947-0.21930.46830.0555-0.08650.26880.02050.320220.6106-57.864857.8086
181.7366-0.66641.89463.8374-1.96072.70850.0132-0.1129-0.0773-0.3490.10160.03320.26760.0295-0.13740.452-0.03670.06870.3402-0.00050.16286.7107-40.456930.9483
192.1701-0.1982-1.20392.87910.05432.61610.0265-0.13130.0163-0.0737-0.0512-0.08260.0454-0.09850.01610.53270.03-0.10870.2520.02820.291911.3851-70.340652.2083
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 27:97)A27 - 97
2X-RAY DIFFRACTION2(chain A and resid 153:337)A153 - 337
3X-RAY DIFFRACTION3(chain A and resid 338:380)A338 - 380
4X-RAY DIFFRACTION4(chain A and resid 381:476)A381 - 476
5X-RAY DIFFRACTION5(chain A and resid 477:515)A477 - 515
6X-RAY DIFFRACTION6(chain B and resid 27:97)B27 - 97
7X-RAY DIFFRACTION7(chain B and resid 153:337)B153 - 337
8X-RAY DIFFRACTION8(chain B and resid 338:379)B338 - 379
9X-RAY DIFFRACTION9(chain B and resid 380:475)B380 - 475
10X-RAY DIFFRACTION10(chain B and resid 476:518)B476 - 518
11X-RAY DIFFRACTION11(chain C and resid 27:96)C27 - 96
12X-RAY DIFFRACTION12(chain C and resid 97:337)C97 - 337
13X-RAY DIFFRACTION13(chain C and resid 338:394)C338 - 394
14X-RAY DIFFRACTION14(chain C and resid 395:478)C395 - 478
15X-RAY DIFFRACTION15(chain C and resid 479:514)C479 - 514
16X-RAY DIFFRACTION16(chain H and resid 1:125)H1 - 125
17X-RAY DIFFRACTION17(chain H and resid 126:214)H126 - 214
18X-RAY DIFFRACTION18(chain L and resid 1:104)L1 - 104
19X-RAY DIFFRACTION19(chain L and resid 105:212)L105 - 212

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