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- PDB-6apd: Crystal structure of RSV F bound by AM22 and the infant antibody ... -

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Basic information

Entry
Database: PDB / ID: 6apd
TitleCrystal structure of RSV F bound by AM22 and the infant antibody ADI-19425
Components
  • AM22 Fab Heavy Chain,IGH@ protein
  • AM22 Fab Light Chain,Uncharacterized protein
  • Fusion glycoprotein F0,Envelope glycoprotein
  • IGL@ protein
  • Immunoglobulin heavy variable 3-21,Immunoglobulin gamma-1 heavy chain
KeywordsIMMUNE SYSTEM / viral glycoprotein / immunoglobulin / infant / complex
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 / immunoglobulin complex / Assembly and release of respiratory syncytial virus (RSV) virions / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / immunoglobulin mediated immune response / antigen binding ...symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / immunoglobulin complex / Assembly and release of respiratory syncytial virus (RSV) virions / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / immunoglobulin mediated immune response / antigen binding / adaptive immune response / 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 / identical protein binding / membrane / metal ion 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 ...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 subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Immunoglobulin heavy variable 3-21 / Fusion glycoprotein F0 / Envelope glycoprotein / Fusion glycoprotein F0 / Immunoglobulin gamma-1 heavy chain / IGL@ protein / IGH@ protein / Ig-like domain-containing protein
Similarity search - Component
Biological speciesRespiratory syncytial virus
Human immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1 Å
AuthorsWrapp, D. / 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 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fusion glycoprotein F0,Envelope glycoprotein
B: Fusion glycoprotein F0,Envelope glycoprotein
C: Fusion glycoprotein F0,Envelope glycoprotein
D: AM22 Fab Heavy Chain,IGH@ protein
E: AM22 Fab Light Chain,Uncharacterized protein
F: AM22 Fab Heavy Chain,IGH@ protein
G: AM22 Fab Light Chain,Uncharacterized protein
H: AM22 Fab Heavy Chain,IGH@ protein
I: AM22 Fab Light Chain,Uncharacterized protein
J: Immunoglobulin heavy variable 3-21,Immunoglobulin gamma-1 heavy chain
K: Immunoglobulin heavy variable 3-21,Immunoglobulin gamma-1 heavy chain
L: IGL@ protein
M: IGL@ protein
N: Immunoglobulin heavy variable 3-21,Immunoglobulin gamma-1 heavy chain
O: IGL@ protein


Theoretical massNumber of molelcules
Total (without water)474,12315
Polymers474,12315
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area47390 Å2
ΔGint-243 kcal/mol
Surface area163470 Å2
Unit cell
Length a, b, c (Å)229.470, 229.470, 304.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain E and resid 1 through 211)
21(chain G and resid 1 through 211)
31chain I
12chain J
22chain K
32chain N
13chain L
23chain M
33chain O
14chain D
24(chain F and resid 1 through 215)
34chain H
15(chain A and (resid 27 through 97 or resid 137 through 515))
25(chain B and (resid 27 through 97 or resid 137 through 515))
35(chain C and resid 27 through 515)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLUARGARG(chain E and resid 1 through 211)EE1 - 2111 - 212
211GLUGLUARGARG(chain G and resid 1 through 211)GG1 - 2111 - 212
311GLUGLUARGARGchain III1 - 2111 - 212
112GLUGLULYSLYSchain JJJ1 - 2141 - 223
212GLUGLULYSLYSchain KKK1 - 2141 - 223
312GLUGLULYSLYSchain NNN1 - 2141 - 223
113SERSERPROPROchain LLL2 - 2092 - 214
213SERSERPROPROchain MMM2 - 2092 - 214
313SERSERPROPROchain OOO2 - 2092 - 214
114GLNGLNSERSERchain DDD1 - 2151 - 226
214GLNGLNSERSER(chain F and resid 1 through 215)FF1 - 2151 - 226
314GLNGLNSERSERchain HHH1 - 2151 - 226
115ASNASNMETMET(chain A and (resid 27 through 97 or resid 137 through 515))AA27 - 9727 - 97
125PHEPHEALAALA(chain A and (resid 27 through 97 or resid 137 through 515))AA137 - 515137 - 515
215ASNASNMETMET(chain B and (resid 27 through 97 or resid 137 through 515))BB27 - 9727 - 97
225PHEPHEALAALA(chain B and (resid 27 through 97 or resid 137 through 515))BB137 - 515137 - 515
315ASNASNALAALA(chain C and resid 27 through 515)CC27 - 51527 - 515

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Protein Fusion glycoprotein F0,Envelope glycoprotein


Mass: 63775.891 Da / Num. of mol.: 3
Mutation: N67I, P129A, S215P, I379V, M447V,N67I, P129A, S215P, I379V, M447V,N67I, P129A, S215P, I379V, M447V,N67I, P129A, S215P, I379V, M447V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Respiratory syncytial virus, (gene. exp.) Human immunodeficiency virus 1
Production host: Homo sapiens (human)
References: UniProt: C3UPB8, UniProt: M1E1E4, UniProt: P03420*PLUS
#2: Antibody AM22 Fab Heavy Chain,IGH@ protein


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 AM22 Fab Light Chain,Uncharacterized protein


Mass: 23304.953 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
#4: Antibody Immunoglobulin heavy variable 3-21,Immunoglobulin gamma-1 heavy chain / Immunoglobulin gamma-1 heavy chain NIE


Mass: 23881.695 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHV3-21 / Production host: Homo sapiens (human) / References: UniProt: A0A0B4J1V1, UniProt: P0DOX5
#5: Antibody IGL@ protein


Mass: 22955.275 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGL@ / Production host: Homo sapiens (human) / References: UniProt: Q6GMX4
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: 4.22 Å3/Da / Density % sol: 70.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 10% PEG 4000 10% 2-propanol 0.1 M sodium citrate pH 5.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97925 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 4.1→50.96 Å / Num. obs: 64175 / % possible obs: 99.9 % / Redundancy: 12.2 % / Biso Wilson estimate: 117.98 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.364 / Rpim(I) all: 0.108 / Rrim(I) all: 0.38 / Net I/σ(I): 6.3 / Num. measured all: 785734 / Scaling rejects: 122
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
4.1-4.2131.5455782144390.6090.4431.6081.9100
18.79-50.968.20.05560567430.9970.0210.0624.994.7

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
Aimless0.5.17data scaling
PDB_EXTRACT3.22data extraction
iMOSFLM7.2.1data reduction
PHASER2.57phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.1→50.958 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2562 3292 5.14 %
Rwork0.2037 60792 -
obs0.2063 64084 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 502 Å2 / Biso mean: 166.2388 Å2 / Biso min: 66.22 Å2
Refinement stepCycle: final / Resolution: 4.1→50.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30005 0 0 0 30005
Num. residues----3968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00330657
X-RAY DIFFRACTIONf_angle_d0.6641703
X-RAY DIFFRACTIONf_chiral_restr0.0464854
X-RAY DIFFRACTIONf_plane_restr0.0055279
X-RAY DIFFRACTIONf_dihedral_angle_d4.93518334
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11E2960X-RAY DIFFRACTION9.34TORSIONAL
12G2960X-RAY DIFFRACTION9.34TORSIONAL
13I2960X-RAY DIFFRACTION9.34TORSIONAL
21J3076X-RAY DIFFRACTION9.34TORSIONAL
22K3076X-RAY DIFFRACTION9.34TORSIONAL
23N3076X-RAY DIFFRACTION9.34TORSIONAL
31L2935X-RAY DIFFRACTION9.34TORSIONAL
32M2935X-RAY DIFFRACTION9.34TORSIONAL
33O2935X-RAY DIFFRACTION9.34TORSIONAL
41D3012X-RAY DIFFRACTION9.34TORSIONAL
42F3012X-RAY DIFFRACTION9.34TORSIONAL
43H3012X-RAY DIFFRACTION9.34TORSIONAL
51A6315X-RAY DIFFRACTION9.34TORSIONAL
52B6315X-RAY DIFFRACTION9.34TORSIONAL
53C6315X-RAY DIFFRACTION9.34TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.1-4.15850.29841210.288124972618100
4.1585-4.22060.34381340.289124702604100
4.2206-4.28650.32791480.271725002648100
4.2865-4.35670.31751500.258624762626100
4.3567-4.43180.26611570.24424772634100
4.4318-4.51240.26011460.227824942640100
4.5124-4.59910.29211310.230825052636100
4.5991-4.69290.28291430.215824922635100
4.6929-4.79490.23621130.207125292642100
4.7949-4.90630.26511340.20525102644100
4.9063-5.02890.27171110.207325232634100
5.0289-5.16480.23971150.204525322647100
5.1648-5.31660.26321430.206225282671100
5.3166-5.4880.26731340.211625112645100
5.488-5.68390.26451250.211825372662100
5.6839-5.91120.26421400.216825292669100
5.9112-6.17980.28371380.206125322670100
6.1798-6.5050.27651420.204225342676100
6.505-6.91160.26741460.191625532699100
6.9116-7.44370.24591450.186725372682100
7.4437-8.19010.24061320.161625832715100
8.1901-9.36880.20641340.152825892723100
9.3688-11.77960.17131390.139926212760100
11.7796-50.96160.26251710.21652733290499
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)
10.72880.30110.23220.9669-0.75242.1662-0.0999-0.10080.3516-0.04360.077-0.0011-0.09830.28440.0410.82760.0157-0.15311.0005-0.13221.139710.148266.0543-36.9534
22.25631.3849-0.00941.52110.08370.31150.0301-0.07040.1707-0.0544-0.05850.01320.03170.10290.02750.90420.0848-0.11381.05010.04091.09320.491448.9789-36.9968
31.57950.3676-0.56740.4657-0.01021.2415-0.2017-0.00910.4656-0.16010.15940.0997-0.09450.05480.04670.67440.0101-0.15490.9443-0.02560.80036.981152.2917-51.1553
43.371.87690.71792.48420.95442.29520.1955-0.6728-1.00090.90770.1307-1.14130.8708-0.2314-0.30421.37420.3068-0.30771.59540.16631.2737-4.029310.573121.6663
52.10722.0255-1.18156.1082-2.1932.32180.2068-0.5651-0.60750.81480.37930.47860.4754-0.6001-0.55781.3060.1279-0.27281.96980.31261.4352-20.98785.734217.1619
62.2778-0.7921-0.84893.1856-0.9546.5004-0.9299-1.29731.29761.18080.573-0.4045-1.153-0.6060.3711.28240.5047-0.35761.9835-0.54681.6853-50.383865.90967.0739
72.9594-3.4009-1.46025.01920.68264.4885-1.5162-2.1299-0.50251.96210.9470.7754-0.1116-0.45480.58011.58320.5423-0.00582.59570.03541.6631-49.599750.209415.9776
89.27232.29060.37012.53180.01432.53530.21190.3084-1.3932-0.4588-0.329-0.28860.3807-0.10080.07561.18440.0613-0.15530.8082-0.0471.322-49.93625.4595-35.1307
95.3042-0.54991.55852.75391.03113.79120.8255-1.1086-0.82120.4628-0.7711.29640.9911-0.7967-0.02141.2876-0.26070.00411.30840.1711.3205-56.78912.2511-19.8171
105.3768-1.57965.61561.0493-0.37546.88890.12770.23230.0167-0.12380.0344-0.1836-0.12750.464-0.18771.001-0.1554-0.09550.76460.03371.0575-22.930845.4411-94.3358
112.6379-1.61260.6964.9949-0.86733.4537-0.17460.0187-0.31060.22010.0748-0.89940.87420.7330.10011.08870.4167-0.22911.3773-0.0191.305456.503313.9432-20.0747
126.9513-0.09813.94230.13220.58935.2902-0.5656-0.15220.0388-0.28050.1012-0.2535-0.6637-0.13120.48980.86-0.04540.01840.63860.00111.1046-33.111257.4432-87.0093
136.3971-0.66911.22364.7693-1.79553.76170.2041-0.4811-1.3399-0.002-0.2615-0.91261.68620.23240.30331.77370.18440.04991.2421-0.12111.363747.30611.9543-29.0375
141.06720.64211.37727.93764.34225.5505-0.2067-0.54780.7238-0.66660.0340.3104-0.9415-0.44210.30851.08490.3439-0.31091.426-0.3251.83087.0815112.4554-11.768
150.68531.1138-0.06352.63351.86933.87240.1648-0.57910.87020.2920.0079-0.1511-0.2576-0.5659-0.20471.03950.3424-0.26061.4424-0.31021.961214.949104.03551.2812
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 27 through 515)A27 - 515
2X-RAY DIFFRACTION2(chain 'B' and resid 27 through 517)B27 - 517
3X-RAY DIFFRACTION3(chain 'C' and resid 27 through 517)C27 - 517
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 215)D1 - 215
5X-RAY DIFFRACTION5(chain 'E' and resid 1 through 212)E1 - 212
6X-RAY DIFFRACTION6(chain 'F' and resid 1 through 216)F1 - 216
7X-RAY DIFFRACTION7(chain 'G' and resid 1 through 214)G1 - 214
8X-RAY DIFFRACTION8(chain 'H' and resid 1 through 215)H1 - 215
9X-RAY DIFFRACTION9(chain 'I' and resid 1 through 211)I1 - 211
10X-RAY DIFFRACTION10(chain 'J' and resid 1 through 214)J1 - 214
11X-RAY DIFFRACTION11(chain 'K' and resid 1 through 214)K1 - 214
12X-RAY DIFFRACTION12(chain 'L' and resid 2 through 209)L2 - 209
13X-RAY DIFFRACTION13(chain 'M' and resid 2 through 209)M2 - 209
14X-RAY DIFFRACTION14(chain 'N' and resid 1 through 214)N1 - 214
15X-RAY DIFFRACTION15(chain 'O' and resid 2 through 209)O2 - 209

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