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- PDB-5en2: Molecular basis for antibody-mediated neutralization of New World... -

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Basic information

Entry
Database: PDB / ID: 5en2
TitleMolecular basis for antibody-mediated neutralization of New World hemorrhagic fever mammarenaviruses
Components
  • GD01 heavy chain
  • GD01 light chain
  • Pre-glycoprotein polyprotein GP complex
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Immunoglobulin / glycoprotein / virus / complex / VIRAL PROTEIN-IMMUNE SYSTEM 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
Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesMus musculus (house mouse)
Junin mammarenavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.821 Å
AuthorsMahmutovic, S. / Clark, L. / Levis, S. / Briggiler, A. / Enria, D. / Harrison, S.C. / Abraham, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI-109740 United States
CitationJournal: Cell Host Microbe / Year: 2015
Title: Molecular Basis for Antibody-Mediated Neutralization of New World Hemorrhagic Fever Mammarenaviruses.
Authors: Mahmutovic, S. / Clark, L. / Levis, S.C. / Briggiler, A.M. / Enria, D.A. / Harrison, S.C. / Abraham, J.
History
DepositionNov 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_radiation_wavelength / 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 / pdbx_unobs_or_zero_occ_atoms / 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 / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _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 2.1Sep 27, 2023Group: 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_initial_refinement_model / struct_conn
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GD01 heavy chain
B: GD01 light chain
C: Pre-glycoprotein polyprotein GP complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8567
Polymers63,9403
Non-polymers1,9164
Water15,961886
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8070 Å2
ΔGint-3 kcal/mol
Surface area27030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.110, 74.790, 177.640
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 , 1 types, 1 molecules C

#3: Protein Pre-glycoprotein polyprotein GP complex


Mass: 16312.702 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Junin mammarenavirus / Gene: GPC, GP-C / Production host: Homo sapiens (human) / References: UniProt: P26313

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Antibody , 2 types, 2 molecules AB

#1: Antibody GD01 heavy chain


Mass: 24167.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#2: Antibody GD01 light chain


Mass: 23459.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)

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Sugars , 3 types, 3 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 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]{}[(6+1)][a-D-2-deoxy-Glcp]{}}}}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#7: 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.: 1
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 , 2 types, 887 molecules

#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 886 / 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: 2.71 Å3/Da / Density % sol: 54.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8
Details: JUNV GP1 and GD01 Fab, when mixed in equimolar ratio crystallized in mother liquor containing 24% PEG 3350 (v/v), 10 mM Tris, pH 8.0, 150 mM NaCl.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9789 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionRedundancy: 5.9 % / Number: 371895 / Rsym value: 0.226 / D res high: 1.821 Å / D res low: 88.82 Å / Num. obs: 63113 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRsym valueRedundancy
5.7668.9310.0680.0685.6
4.075.7610.0720.0725.7
3.324.0710.0890.0896.1
2.883.3210.1330.1336
2.582.8810.2080.2086.1
2.352.5810.3240.3245.8
2.182.3510.4550.4556.2
2.042.1810.640.645.6
1.922.0410.950.956
1.821.9211.4181.4185.7
ReflectionResolution: 1.821→68.93 Å / Num. all: 63113 / Num. obs: 63113 / % possible obs: 99.9 % / Redundancy: 5.9 % / Biso Wilson estimate: 20.23 Å2 / Rpim(I) all: 0.101 / Rrim(I) all: 0.248 / Rsym value: 0.226 / Net I/av σ(I): 3.125 / Net I/σ(I): 6.7 / Num. measured all: 371895
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.82-1.925.71.4180.55145490750.6481.4181.599.9
1.92-2.0460.950.75173485990.4190.952.2100
2.04-2.185.60.641.14527081260.2950.64399.9
2.18-2.356.20.4551.64673975580.1970.4554.2100
2.35-2.585.80.3242.34065169800.1450.3245.499.9
2.58-2.886.10.2083.53895863560.0910.2087.7100
2.88-3.3260.1335.43345156100.0590.13311.399.9
3.32-4.076.10.0897.92938048040.0390.08916.499.9
4.07-5.765.70.0729.12177537940.0320.07218.299.9
5.76-68.935.60.0688.41248322110.0310.06816.499.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.82 Å68.93 Å
Translation1.82 Å68.93 Å

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Processing

Software
NameVersionClassification
BUSTER-TNTBUSTER 2.10.2refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASER2.5.5phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KAS, 3FMG

3kas

3fmg


Resolution: 1.821→68.93 Å / Cor.coef. Fo:Fc: 0.9458 / Cor.coef. Fo:Fc free: 0.9137 / SU R Cruickshank DPI: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.138 / SU Rfree Blow DPI: 0.13 / SU Rfree Cruickshank DPI: 0.12
RfactorNum. reflection% reflectionSelection details
Rfree0.2244 3168 5.03 %RANDOM
Rwork0.1805 ---
obs0.1827 63032 99.69 %-
Displacement parametersBiso max: 163.53 Å2 / Biso mean: 25.51 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-2.0897 Å20 Å20 Å2
2---0.42 Å20 Å2
3----1.6697 Å2
Refine analyzeLuzzati coordinate error obs: 0.218 Å
Refinement stepCycle: final / Resolution: 1.821→68.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4459 0 125 886 5470
Biso mean--56.78 39.57 -
Num. residues----572
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1601SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes99HARMONIC2
X-RAY DIFFRACTIONt_gen_planes672HARMONIC5
X-RAY DIFFRACTIONt_it4718HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion656SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5905SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4718HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6433HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion3.86
X-RAY DIFFRACTIONt_other_torsion15.33
LS refinement shellResolution: 1.82→1.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 229 5.09 %
Rwork0.2388 4269 -
all0.2406 4498 -
obs--97.33 %

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