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- PDB-5wnb: Structure of antibody 3D3 bound to the linear epitope of RSV G -

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Basic information

Entry
Database: PDB / ID: 5wnb
TitleStructure of antibody 3D3 bound to the linear epitope of RSV G
Components
  • Major surface glycoprotein G
  • mAb 3D3 Fab heavy chain
  • mAb 3D3 Fab light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / RSV / glycoprotein / G glycoprotein / viral protein / viral attachment protein / antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


adhesion receptor-mediated virion attachment to host cell / virus-mediated perturbation of host defense response / symbiont entry into host cell / host cell plasma membrane / virion membrane / extracellular region / membrane
Similarity search - Function
Major surface glycoprotein G / Pneumovirus attachment glycoprotein G / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETIC ACID / Major surface glycoprotein G
Similarity search - Component
Biological speciesHomo sapiens (human)
Human respiratory syncytial virus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsFedechkin, S.O. / George, N.L. / Wolff, J.T. / Kauvar, L.M. / DuBois, R.M.
CitationJournal: Sci Immunol / Year: 2018
Title: Structures of respiratory syncytial virus G antigen bound to broadly neutralizing antibodies.
Authors: Fedechkin, S.O. / George, N.L. / Wolff, J.T. / Kauvar, L.M. / DuBois, R.M.
History
DepositionJul 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: mAb 3D3 Fab heavy chain
L: mAb 3D3 Fab light chain
I: mAb 3D3 Fab heavy chain
M: mAb 3D3 Fab light chain
A: Major surface glycoprotein G
B: Major surface glycoprotein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,36522
Polymers99,3296
Non-polymers1,03616
Water1,62190
1
H: mAb 3D3 Fab heavy chain
L: mAb 3D3 Fab light chain
B: Major surface glycoprotein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,24812
Polymers49,6643
Non-polymers5839
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-40 kcal/mol
Surface area19460 Å2
MethodPISA
2
I: mAb 3D3 Fab heavy chain
M: mAb 3D3 Fab light chain
A: Major surface glycoprotein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,11710
Polymers49,6643
Non-polymers4537
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-37 kcal/mol
Surface area18830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.760, 105.430, 121.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein/peptide , 1 types, 2 molecules AB

#3: Protein/peptide Major surface glycoprotein G / Attachment glycoprotein G / Membrane-bound glycoprotein / mG


Mass: 1398.538 Da / Num. of mol.: 2
Fragment: Central conserved region of RSV G, UNP residues 162-172
Source method: obtained synthetically / Source: (synth.) Human respiratory syncytial virus A / References: UniProt: P03423

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Antibody , 2 types, 4 molecules HILM

#1: Antibody mAb 3D3 Fab heavy chain


Mass: 24778.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody mAb 3D3 Fab light chain


Mass: 23487.041 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Non-polymers , 3 types, 106 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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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: 2.22 Å3/Da / Density % sol: 44.66 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 23% PEG 3350, 0.05 M zinc acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11503 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 17, 2016 / Details: Pilatus3 S, 25Hz, S/N 60-0134
RadiationMonochromator: Si(111) Khozu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11503 Å / Relative weight: 1
ReflectionResolution: 2.3→48.38 Å / Num. obs: 40103 / % possible obs: 99.9 % / Redundancy: 9.2 % / Biso Wilson estimate: 37.52 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.045 / Rrim(I) all: 0.138 / Net I/σ(I): 13.4 / Num. measured all: 368399 / Scaling rejects: 7
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
2.3-2.388.91.1543448238660.7490.4061.2252.7100
8.91-48.389.10.0572477930.9980.0170.0533299.4

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I30

5i30


Resolution: 2.4→48.38 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.87 / Stereochemistry target values: ML / Details: PHENIX
RfactorNum. reflection% reflection
Rfree0.2682 1763 4.99 %
Rwork0.2241 33562 -
obs0.2263 35325 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.31 Å2 / Biso mean: 49.2866 Å2 / Biso min: 14.49 Å2
Refinement stepCycle: final / Resolution: 2.4→48.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6549 0 22 90 6661
Biso mean--63.15 34.99 -
Num. residues----877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056723
X-RAY DIFFRACTIONf_angle_d0.8839169
X-RAY DIFFRACTIONf_chiral_restr0.0561039
X-RAY DIFFRACTIONf_plane_restr0.0081180
X-RAY DIFFRACTIONf_dihedral_angle_d18.1452339
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4-2.46490.32651330.297325502683
2.4649-2.53740.28841330.281925232656
2.5374-2.61930.34711330.271525352668
2.6193-2.71290.32771340.260225392673
2.7129-2.82160.29371340.264325612695
2.8216-2.950.32791350.258425602695
2.95-3.10550.31621350.250725632698
3.1055-3.30.2551350.242325732708
3.3-3.55470.25511330.2225582691
3.5547-3.91230.27531380.212726012739
3.9123-4.4780.22671360.186126052741
4.478-5.64050.23161380.177826312769
5.6405-48.38940.24611460.222727632909
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)
12.655-0.7258-0.61144.3230.25911.9190.1215-0.07780.22250.2957-0.1032-0.1850.01180.0770.02090.18840.05580.01710.27720.10070.3314-16.07718.7344-33.5542
23.435-0.45760.00071.8908-0.10411.14310.03560.32140.3157-0.1743-0.11350.00430.0552-0.04330.01830.25090.06470.02720.22630.11880.2959-13.591218.8194-40.0314
33.8101-1.62370.02563.3515-1.32283.1659-0.1339-0.3740.54230.81730.1127-0.3355-0.18740.23790.00170.36560.0266-0.04360.2155-0.06050.2922-22.8574-6.9074-14.082
45.3088-5.50433.56478.9027-5.36475.5391-0.11710.0859-0.6894-0.1701-0.0583-0.1370.26290.15140.02770.42580.08810.16010.20540.04380.4096-2.7709-4.6248-42.465
53.039-0.3026-1.27282.7423-0.65981.24140.04240.3243-0.3028-0.4236-0.3844-0.30570.01720.23740.19480.29680.10150.12910.34460.11950.26760.99584.2782-41.6555
62.0110.2816-0.1652.2613-1.47641.17850.1374-0.1217-0.3363-0.0646-0.5107-0.2743-0.02180.33360.28050.25030.03190.00230.1558-0.05420.2079-15.6996-7.4205-29.9741
79.60841.2437-1.30631.8989-0.68262.40160.18220.2253-0.4949-0.3655-0.1079-0.62650.0752-0.0302-0.08010.25050.01510.0330.14580.04970.3258-20.4517-18.0183-26.5314
89.62616.511-0.93935.3597-1.24831.7185-0.08820.3239-0.3207-0.56260.0845-0.05160.3374-0.2115-0.20260.29910.0250.05050.37820.04090.2397-28.9704-18.2154-30.2196
96.89522.4539-1.70622.8916-0.79091.3791-0.14350.20370.0269-0.037-0.042-0.40630.20980.03670.13540.25390.00610.01880.23990.02960.3478-23.6719-20.1899-23.7016
104.3535-1.8517-0.36322.5162-0.49832.4281-0.0189-0.2242-0.36520.1590.44660.9287-0.1066-0.4659-0.13950.36750.0673-0.0020.47590.08270.4117-0.1546-10.61823.6765
112.8368-0.43870.09770.8534-0.19160.06390.0188-0.64290.27740.52190.0709-0.0321-0.8041-0.2741-0.01180.6320.16940.03990.3586-0.0430.21939.4977-6.49957.2756
122.13790.12190.42273.27190.33973.25980.1213-0.235-0.00820.09540.2531-0.0462-0.3339-0.3197-0.21510.33460.08560.05640.33750.05510.17948.2874-9.64791.2515
130.5784-0.12820.97820.3335-0.37711.7274-0.5985-0.54410.33140.93760.15080.4388-0.7623-0.5852-0.00610.84440.49830.04250.9653-0.05170.4908-8.519817.9181-2.2773
143.99271.5845-1.2240.7-0.94213.263-1.1313-0.1052-0.47571.2160.23670.75650.2484-0.42970.16160.98370.43690.11460.62510.00470.5738-12.023514.6656-5.2668
151.01040.52721.21890.53451.58395.0403-0.8909-0.94550.08490.82740.17620.4029-0.179-0.38120.21810.88820.4322-0.09040.7129-0.03750.4269-5.28818.0329-5.6526
164.0472-0.3508-0.11423.25330.11262.3248-0.19970.00270.05460.87250.2230.5595-0.6547-0.12210.1360.74180.213-0.11370.621-0.06450.5113-13.412223.2364-14.3481
176.7248-2.72930.74071.70850.78212.0344-0.6985-0.4499-1.10851.03410.19030.5092-0.5701-0.30420.4590.88170.46940.08121.08890.07930.579-18.590818.9019-5.0011
184.4921-0.85243.71715.01520.24715.9913-0.2360.27360.72880.1784-0.3471-1.0323-0.09520.40620.56620.44970.0150.03860.24290.08270.547719.74976.9438-12.7946
193.5588-2.40242.314.4482-2.49445.9758-0.04440.26190.38320.0627-0.065-0.2861-0.38940.06150.140.283-0.00660.0860.21690.02280.261617.9645-2.4968-12.9479
201.0615-0.88240.75262.45380.13751.3972-0.35890.14390.64320.213-0.0668-0.1079-0.5491-0.36080.38560.50790.0564-0.09480.4310.0610.559610.058513.5202-9.6298
213.3093-1.4206-1.84893.77121.35894.4528-0.3215-0.50830.94190.44310.2016-0.6-0.4942-0.14290.16560.74840.2756-0.23820.5904-0.10680.65481.524328.7736-6.2466
226.9122-0.6914-1.62025.97947.14529.1041-0.6457-0.28590.2295-0.04530.4870.3022-0.7779-0.31640.17710.67770.1275-0.06540.34760.05560.50313.56618.1737-13.9698
230.0910.03670.1852.16470.60820.5387-0.4849-0.67860.97690.04960.4587-0.7958-0.38860.222-1.15521.2010.2731-0.36450.5297-0.36721.03152.093734.9253-5.9028
243.0509-0.0167-2.73725.76322.15653.49070.341-0.0754-0.26250.60440.0611-0.18940.76660.3394-0.54720.37370.0403-0.09410.24980.02920.205419.664-16.9232.4406
257.613-0.58750.5634.71992.14654.91230.19360.87290.3328-0.6358-0.5364-0.7514-1.03760.49570.22090.40380.09040.09910.45040.27110.5199-4.083623.0483-49.9977
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 44 )H1 - 44
2X-RAY DIFFRACTION2chain 'H' and (resid 45 through 122 )H45 - 122
3X-RAY DIFFRACTION3chain 'H' and (resid 123 through 227 )H123 - 227
4X-RAY DIFFRACTION4chain 'L' and (resid 1 through 18 )L1 - 18
5X-RAY DIFFRACTION5chain 'L' and (resid 19 through 90 )L19 - 90
6X-RAY DIFFRACTION6chain 'L' and (resid 91 through 127 )L91 - 127
7X-RAY DIFFRACTION7chain 'L' and (resid 128 through 149 )L128 - 149
8X-RAY DIFFRACTION8chain 'L' and (resid 150 through 162 )L150 - 162
9X-RAY DIFFRACTION9chain 'L' and (resid 163 through 213 )L163 - 213
10X-RAY DIFFRACTION10chain 'I' and (resid 1 through 33 )I1 - 33
11X-RAY DIFFRACTION11chain 'I' and (resid 34 through 73 )I34 - 73
12X-RAY DIFFRACTION12chain 'I' and (resid 74 through 114 )I74 - 114
13X-RAY DIFFRACTION13chain 'I' and (resid 115 through 154 )I115 - 154
14X-RAY DIFFRACTION14chain 'I' and (resid 155 through 168 )I155 - 168
15X-RAY DIFFRACTION15chain 'I' and (resid 169 through 188 )I169 - 188
16X-RAY DIFFRACTION16chain 'I' and (resid 189 through 211 )I189 - 211
17X-RAY DIFFRACTION17chain 'I' and (resid 212 through 225 )I212 - 225
18X-RAY DIFFRACTION18chain 'M' and (resid 1 through 18 )M1 - 18
19X-RAY DIFFRACTION19chain 'M' and (resid 19 through 90 )M19 - 90
20X-RAY DIFFRACTION20chain 'M' and (resid 91 through 120 )M91 - 120
21X-RAY DIFFRACTION21chain 'M' and (resid 121 through 157 )M121 - 157
22X-RAY DIFFRACTION22chain 'M' and (resid 158 through 173 )M158 - 173
23X-RAY DIFFRACTION23chain 'M' and (resid 174 through 210 )M174 - 210
24X-RAY DIFFRACTION24chain 'A' and (resid 162 through 172 )A162 - 172
25X-RAY DIFFRACTION25chain 'B' and (resid 162 through 172 )B162 - 172

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