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Basic information

Entry
Database: PDB / ID: 6lgw
TitleStructure of Rabies virus glycoprotein in complex with neutralizing antibody 523-11 at acidic pH
Components
  • Glycoprotein
  • scFv 523-11
KeywordsVIRAL PROTEIN / functional class
Function / homologyRhabdovirus glycoprotein / Rhabdovirus spike glycoprotein / viral envelope / virion membrane / membrane / Glycoprotein / Glycoprotein / Glycoprotein / Glycoprotein
Function and homology information
Biological speciesMus musculus (house mouse)
Lyssavirus rabies
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9037 Å
AuthorsYang, F.L. / Lin, S. / Ye, F. / Yang, J. / Qi, J.X. / Chen, Z.J. / Lin, X. / Wang, J.C. / Yue, D. / Cheng, Y.W. ...Yang, F.L. / Lin, S. / Ye, F. / Yang, J. / Qi, J.X. / Chen, Z.J. / Lin, X. / Wang, J.C. / Yue, D. / Cheng, Y.W. / Chen, Z.M. / Chen, H. / You, Y. / Zhang, Z.L. / Yang, Y. / Yang, M. / Sun, H.L. / Li, Y.H. / Cao, Y. / Yang, S.Y. / Wei, Y.Q. / Gao, G.F. / Lu, G.W.
CitationJournal: Cell Host Microbe / Year: 2020
Title: Structural Analysis of Rabies Virus Glycoprotein Reveals pH-Dependent Conformational Changes and Interactions with a Neutralizing Antibody.
Authors: Yang, F. / Lin, S. / Ye, F. / Yang, J. / Qi, J. / Chen, Z. / Lin, X. / Wang, J. / Yue, D. / Cheng, Y. / Chen, Z. / Chen, H. / You, Y. / Zhang, Z. / Yang, Y. / Yang, M. / Sun, H. / Li, Y. / ...Authors: Yang, F. / Lin, S. / Ye, F. / Yang, J. / Qi, J. / Chen, Z. / Lin, X. / Wang, J. / Yue, D. / Cheng, Y. / Chen, Z. / Chen, H. / You, Y. / Zhang, Z. / Yang, Y. / Yang, M. / Sun, H. / Li, Y. / Cao, Y. / Yang, S. / Wei, Y. / Gao, G.F. / Lu, G.
History
DepositionDec 6, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Nov 22, 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 2.0Mar 13, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / refine_ls_restr_ncs / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ncs_dom / struct_ncs_dom_lim / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_seq_id / _entity_poly_seq.entity_id / _entity_poly_seq.num / _pdbx_poly_seq_scheme.asym_id / _pdbx_poly_seq_scheme.entity_id / _pdbx_poly_seq_scheme.ndb_seq_num / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.seq_id / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_refine_tls_group.beg_auth_asym_id / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_refine_tls_group.selection_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_asym_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_asym_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.label_asym_id / _pdbx_unobs_or_zero_occ_residues.label_seq_id / _pdbx_validate_torsion.auth_asym_id / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_asym_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_asym_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_asym_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_mon_prot_cis.auth_asym_id / _struct_mon_prot_cis.auth_seq_id / _struct_mon_prot_cis.label_asym_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_auth_asym_id_2 / _struct_mon_prot_cis.pdbx_auth_seq_id_2 / _struct_mon_prot_cis.pdbx_label_asym_id_2 / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref_seq_dif.align_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_asym_id / _struct_sheet_range.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: scFv 523-11
E: Glycoprotein
C: scFv 523-11
F: Glycoprotein


Theoretical massNumber of molelcules
Total (without water)142,0224
Polymers142,0224
Non-polymers00
Water00
1
A: scFv 523-11
E: Glycoprotein


Theoretical massNumber of molelcules
Total (without water)71,0112
Polymers71,0112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-14 kcal/mol
Surface area31280 Å2
MethodPISA
2
C: scFv 523-11
F: Glycoprotein


Theoretical massNumber of molelcules
Total (without water)71,0112
Polymers71,0112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-15 kcal/mol
Surface area31860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.892, 93.943, 213.491
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
12(chain A and (resseq 1:12 or resseq 14:31 or (resid...
22(chain C and ((resid 1 and (name N or name...

NCS domain segments:

Ens-ID: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUVALVAL(chain A and (resseq 1:12 or resseq 14:31 or (resid...AA1 - 121 - 12
12PROPROASPASP(chain A and (resseq 1:12 or resseq 14:31 or (resid...AA14 - 3114 - 31
13TYRTYRTYRTYR(chain A and (resseq 1:12 or resseq 14:31 or (resid...AA3232
14GLUGLUSERSER(chain A and (resseq 1:12 or resseq 14:31 or (resid...AA1 - 1181 - 118
15GLUGLUSERSER(chain A and (resseq 1:12 or resseq 14:31 or (resid...AA1 - 1181 - 118
16GLUGLUSERSER(chain A and (resseq 1:12 or resseq 14:31 or (resid...AA1 - 1181 - 118
17GLUGLUSERSER(chain A and (resseq 1:12 or resseq 14:31 or (resid...AA1 - 1181 - 118
18GLUGLUSERSER(chain A and (resseq 1:12 or resseq 14:31 or (resid...AA1 - 1181 - 118
19GLUGLUSERSER(chain A and (resseq 1:12 or resseq 14:31 or (resid...AA1 - 1181 - 118
110GLUGLUSERSER(chain A and (resseq 1:12 or resseq 14:31 or (resid...AA1 - 1181 - 118
21GLUGLUGLUGLU(chain C and ((resid 1 and (name N or name...CC11
22GLUGLUSERSER(chain C and ((resid 1 and (name N or name...CC1 - 1191 - 119
23GLUGLUSERSER(chain C and ((resid 1 and (name N or name...CC1 - 1191 - 119
24GLUGLUSERSER(chain C and ((resid 1 and (name N or name...CC1 - 1191 - 119
25GLUGLUSERSER(chain C and ((resid 1 and (name N or name...CC1 - 1191 - 119
26GLUGLUSERSER(chain C and ((resid 1 and (name N or name...CC1 - 1191 - 119
27GLUGLUSERSER(chain C and ((resid 1 and (name N or name...CC1 - 1191 - 119
28GLUGLUSERSER(chain C and ((resid 1 and (name N or name...CC1 - 1191 - 119

NCS ensembles :
ID
1
2

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Components

#1: Antibody scFv 523-11


Mass: 25196.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Protein Glycoprotein


Mass: 45815.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lyssavirus rabies / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q5JZZ2, UniProt: Q2Z2I1, UniProt: D8VEC1

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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: 2.93 Å3/Da / Density % sol: 57.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30 mM Diethylene glycol, 30 mM Triethylene glycol, 30 mM Tetraethylene glycol, 30 mM Pentaethylene glycol, 55.5 mM MES monohydrate, 44.5 mM Imidazole, 20% v/v Ethylene glycol, 10% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 37561 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.9 % / Biso Wilson estimate: 83.35 Å2 / CC1/2: 0.982 / Net I/σ(I): 14.76
Reflection shellResolution: 2.9→3 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 0.96 / Num. unique obs: 3681 / CC1/2: 0.514 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.16-3549refinement
PDB_EXTRACTdata extraction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M43

4m43


Resolution: 2.9037→46.9776 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.16
RfactorNum. reflection% reflection
Rfree0.2684 1863 4.97 %
Rwork0.2176 --
obs0.2202 37497 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 207.01 Å2 / Biso mean: 96.7358 Å2 / Biso min: 43.04 Å2
Refinement stepCycle: final / Resolution: 2.9037→46.9776 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9342 0 0 0 9342
Num. residues----1191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049583
X-RAY DIFFRACTIONf_angle_d0.70712993
X-RAY DIFFRACTIONf_chiral_restr0.0471423
X-RAY DIFFRACTIONf_plane_restr0.0051647
X-RAY DIFFRACTIONf_dihedral_angle_d15.7225746
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
21A995X-RAY DIFFRACTION13.529TORSIONAL
22C995X-RAY DIFFRACTION13.529TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9037-2.98220.44131340.3592259795
2.9822-3.06990.381350.29632720100
3.0699-3.1690.33611270.27722699100
3.169-3.28220.35121430.2572718100
3.2822-3.41360.32571210.25512727100
3.4136-3.56890.30871670.24232698100
3.5689-3.7570.32741450.21292747100
3.757-3.99220.25851260.19952719100
3.9922-4.30030.26241410.18412751100
4.3003-4.73270.19621560.17152747100
4.7327-5.41670.2371500.18052772100
5.4167-6.82110.28881510.23342812100
6.8211-46.97760.23311670.22512927100
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)
13.22330.73610.37762.4349-0.09061.5639-0.09320.9574-0.0689-0.29870.39420.44760.1628-0.0774-0.30740.5905-0.0622-0.12971.17380.01720.9674-1.54-45.495-86.688
22.6706-0.09610.11962.02960.56761.3992-0.05570.17470.8779-0.06640.20631.1382-0.5206-0.4579-0.16990.80340.06520.08720.92710.18891.5478-13.702-27.362-81.433
33.42970.3016-0.15222.49510.44921.81170.1684-0.09230.0932-0.0699-0.0442-0.4541-0.3140.3537-0.13680.6236-0.06990.02680.53350.11940.657326.878-26.30238.082
42.84960.1779-0.57212.9822-1.53132.16550.18820.06161.0755-0.1816-0.15750.0538-0.782-0.1421-0.04480.81580.04550.09010.41950.10250.809711.93-9.77836.065
51.19560.0708-0.52380.0221-0.37363.31970.04760.01440.08820.08620.0256-0.070.1047-0.5755-0.08220.6031-0.06090.02480.4815-0.06670.668313.968-36.862-51.358
6-0.12720.1613-0.77680.175-0.82963.0148-0.00020.1279-0.0333-0.06490.16450.0702-0.0332-0.4033-0.17310.6385-0.04440.00080.70450.10230.556512.156-39.0047.626
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:118 )A1 - 118
2X-RAY DIFFRACTION2( CHAIN A AND RESID 121:224 )A121 - 224
3X-RAY DIFFRACTION3( CHAIN C AND RESID 1:119 )C1 - 119
4X-RAY DIFFRACTION4( CHAIN C AND RESID 121:224 )C121 - 224
5X-RAY DIFFRACTION5( CHAIN E AND RESID 1:395 )E1 - 395
6X-RAY DIFFRACTION6( CHAIN F AND RESID 1:397 )F1 - 397

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