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- PDB-5nuz: Junin virus GP1 glycoprotein in complex with an antibody Fab fragment -

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Basic information

Entry
Database: PDB / ID: 5nuz
TitleJunin virus GP1 glycoprotein in complex with an antibody Fab fragment
Components
  • Pre-glycoprotein polyprotein GP complex
  • eOD01 heavy chain
  • eOD01 light chain
KeywordsIMMUNE SYSTEM / viral antigen-antibody complex
Function / homology
Function and homology information


host cell Golgi membrane / receptor-mediated endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane / metal ion binding
Similarity search - Function
Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesMus musculus (house mouse)
Junin mammarenavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsZeltina, A. / Krumm, S.A. / Sahin, M. / Struwe, W.B. / Harlos, K. / Nunberg, J.H. / Crispin, M. / Pinschewer, D.D. / Doores, K.J. / Bowden, T.A.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Convergent immunological solutions to Argentine hemorrhagic fever virus neutralization.
Authors: Zeltina, A. / Krumm, S.A. / Sahin, M. / Struwe, W.B. / Harlos, K. / Nunberg, J.H. / Crispin, M. / Pinschewer, D.D. / Doores, K.J. / Bowden, T.A.
History
DepositionMay 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: eOD01 heavy chain
H: eOD01 heavy chain
B: eOD01 light chain
C: Pre-glycoprotein polyprotein GP complex
L: eOD01 light chain
D: Pre-glycoprotein polyprotein GP complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,48828
Polymers134,8196
Non-polymers4,67022
Water16,214900
1
A: eOD01 heavy chain
B: eOD01 light chain
C: Pre-glycoprotein polyprotein GP complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,46814
Polymers67,4093
Non-polymers2,05911
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: eOD01 heavy chain
L: eOD01 light chain
D: Pre-glycoprotein polyprotein GP complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,02014
Polymers67,4093
Non-polymers2,61111
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.090, 101.910, 147.760
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
11A
21H
12B
22L
13C
23D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUASPASPAA1 - 2144 - 224
21GLUGLUASPASPHB1 - 2144 - 224
12GLYGLYASNASNBC0 - 2123 - 219
22GLYGLYASNASNLE0 - 2123 - 219
13LEULEUASPASPCD88 - 2295 - 146
23LEULEUASPASPDF88 - 2295 - 146

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 2 molecules CD

#3: Protein Pre-glycoprotein polyprotein GP complex


Mass: 18095.586 Da / Num. of mol.: 2 / Fragment: receptor attachment glycoprotein GP1
Source method: isolated from a genetically manipulated source
Details: Fragment: receptor attachment glycoprotein GP1, residues 87-232
Source: (gene. exp.) Junin mammarenavirus / Gene: GPC / Plasmid: pOPINTTGNeo / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: C1K9J9

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Antibody , 2 types, 4 molecules AHBL

#1: Antibody eOD01 heavy chain


Mass: 25127.076 Da / Num. of mol.: 2
Fragment: Fab fragment (domains: variable heavy and constant heavy 1)
Source method: isolated from a genetically manipulated source
Details: Fab fragment (domains: variable heavy and constant heavy 1)
Source: (gene. exp.) Mus musculus (house mouse) / Variant: BALB/c / Plasmid: pHLsec / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#2: Antibody eOD01 light chain


Mass: 24186.633 Da / Num. of mol.: 2
Fragment: Fab fragment (domains: variable light and constant light)
Source method: isolated from a genetically manipulated source
Details: Fab fragment (domains: variable light and constant light)
Source: (gene. exp.) Mus musculus (house mouse) / Variant: BALB/c / Plasmid: pHLsec / Cell line (production host): HEK293T / Production host: Homo sapiens (human)

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Sugars , 3 types, 5 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1559.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6[DManpa1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-h1_h2-i1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#8: 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


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 , 3 types, 917 molecules

#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 900 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.71 Å3/Da / Density % sol: 54.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 20 % (v/v) 2-propanol, 20 % (w/v) PEG 4000, 0.1 M tri-Sodium Citrate (pH 5.6)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 10, 2015
Details: Kirkpatrick Baez (KB) bimorph mirror pair for horizontal and vertical focussing
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.85→50.93 Å / Num. obs: 124898 / % possible obs: 99.7 % / Redundancy: 11.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.131 / Net I/σ(I): 15.6
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 12 % / Rmerge(I) obs: 1.78 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 9101 / CC1/2: 0.669 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
xia2data reduction
PHASERphasing
Cootmodel building
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→50.93 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 5.959 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.116
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES, WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2099 6121 4.9 %RANDOM
Rwork0.1845 ---
obs0.1858 118415 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 105.86 Å2 / Biso mean: 36.176 Å2 / Biso min: 18.18 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å20 Å2-0 Å2
2---1.99 Å20 Å2
3---0.39 Å2
Refinement stepCycle: final / Resolution: 1.85→50.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8935 0 309 900 10144
Biso mean--65.51 42.87 -
Num. residues----1151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.029536
X-RAY DIFFRACTIONr_bond_other_d0.0020.028406
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.97412986
X-RAY DIFFRACTIONr_angle_other_deg0.8723.00119706
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9045.0561160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.25624.593381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.827151484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2871530
X-RAY DIFFRACTIONr_chiral_restr0.0770.21484
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110262
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021844
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A133760.04
12H133760.04
21B134780.05
22L134780.05
31C88600.09
32D88600.09
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 444 -
Rwork0.312 8581 -
all-9025 -
obs--98.86 %
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)
10.06790.1626-0.09331.5231-0.18180.2601-0.00930.0027-0.02580.05770.05320.1284-0.04710.0342-0.04390.0481-0.00210.04090.06720.00930.134-7.39649.226115.2355
20.1419-0.0134-0.05561.34290.21040.2106-0.02860.02950.00490.12370.03720.0650.01610.0291-0.00860.0727-0.00240.04180.0873-0.01310.072921.479516.229144.0782
30.20220.2898-0.0940.8401-0.28170.1418-0.04870.0851-0.0525-0.15040.0576-0.0047-0.00230.0136-0.00890.0896-0.03050.01340.112-0.03230.07584.43575.01042.0743
42.94671.0716-1.10490.9716-1.4092.61070.46840.2670.09330.5139-0.14010.1261-0.60650.1508-0.32820.3745-0.12660.07680.14750.01330.10626.400254.00888.0154
50.0987-0.1021-0.00710.64790.33380.4284-0.0091-0.0051-0.009-0.07040.0535-0.0264-0.06090.1501-0.04440.0317-0.04350.03660.1403-0.03590.081434.60720.393632.4764
61.3457-0.4763-0.96981.17220.6831.7592-0.03240.0814-0.14130.2023-0.11810.11870.23630.04030.15050.18440.02550.03380.0559-0.04850.098328.1597-27.721628.6948
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 214
2X-RAY DIFFRACTION2H1 - 214
3X-RAY DIFFRACTION3B0 - 213
4X-RAY DIFFRACTION4C88 - 229
5X-RAY DIFFRACTION5L-1 - 213
6X-RAY DIFFRACTION6D88 - 229

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