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- PDB-5w1k: JUNV GP1 CR1-10 Fab CR1-28 Fab complex -

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Basic information

Entry
Database: PDB / ID: 5w1k
TitleJUNV GP1 CR1-10 Fab CR1-28 Fab complex
Components
  • CR1-10 Fab heavy chain
  • CR1-10 Fab light chain
  • CR1-28 Fab heavy chain
  • CR1-28 Fab light chain
  • Pre-glycoprotein polyprotein GP complex
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Fab / antibody / Junin virus / arenavirus / viral protein / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell Golgi membrane / immunoglobulin complex / receptor-mediated endocytosis of virus by host cell / adaptive immune response / 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 ...host cell Golgi membrane / immunoglobulin complex / receptor-mediated endocytosis of virus by host cell / adaptive immune response / 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 / extracellular region / metal ion binding / membrane / plasma membrane
Similarity search - Function
Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein / : / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein / : / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin kappa light chain / Pre-glycoprotein polyprotein GP complex / IGK@ protein / IgG H chain / IgG H chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Junin mammarenavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.99 Å
AuthorsRaymond, D.D. / Clark, L.E. / Abraham, J.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorDP5OD023084 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI007061 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI109740 United States
Other privateBurroughs Wellcome Fund United States
Other privateWilliam Randolph Hearst Foundation and Brigham and Womens Hospital United States
Other privateHarvard Medical School DICP United States
CitationJournal: Nat Commun / Year: 2018
Title: Vaccine-elicited receptor-binding site antibodies neutralize two New World hemorrhagic fever arenaviruses.
Authors: Clark, L.E. / Mahmutovic, S. / Raymond, D.D. / Dilanyan, T. / Koma, T. / Manning, J.T. / Shankar, S. / Levis, S.C. / Briggiler, A.M. / Enria, D.A. / Wucherpfennig, K.W. / Paessler, S. / Abraham, J.
History
DepositionJun 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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.Cartn_x / _atom_site.Cartn_y ..._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 / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CR1-28 Fab light chain
B: CR1-28 Fab heavy chain
C: CR1-10 Fab light chain
D: CR1-10 Fab heavy chain
E: Pre-glycoprotein polyprotein GP complex
F: CR1-28 Fab light chain
G: CR1-28 Fab heavy chain
H: CR1-10 Fab light chain
I: CR1-10 Fab heavy chain
J: Pre-glycoprotein polyprotein GP complex
K: CR1-28 Fab light chain
L: CR1-28 Fab heavy chain
M: CR1-10 Fab light chain
N: CR1-10 Fab light chain
O: CR1-10 Fab heavy chain
P: Pre-glycoprotein polyprotein GP complex
Q: CR1-10 Fab heavy chain
R: Pre-glycoprotein polyprotein GP complex
S: CR1-28 Fab light chain
T: CR1-28 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)443,00925
Polymers440,60420
Non-polymers2,4055
Water00
1
A: CR1-28 Fab light chain
B: CR1-28 Fab heavy chain
N: CR1-10 Fab light chain
O: CR1-10 Fab heavy chain
P: Pre-glycoprotein polyprotein GP complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,9597
Polymers110,1515
Non-polymers8082
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: CR1-10 Fab light chain
D: CR1-10 Fab heavy chain
E: Pre-glycoprotein polyprotein GP complex
F: CR1-28 Fab light chain
G: CR1-28 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,7386
Polymers110,1515
Non-polymers5871
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
H: CR1-10 Fab light chain
I: CR1-10 Fab heavy chain
J: Pre-glycoprotein polyprotein GP complex
K: CR1-28 Fab light chain
L: CR1-28 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,5756
Polymers110,1515
Non-polymers4241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
M: CR1-10 Fab light chain
Q: CR1-10 Fab heavy chain
R: Pre-glycoprotein polyprotein GP complex
S: CR1-28 Fab light chain
T: CR1-28 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,7386
Polymers110,1515
Non-polymers5871
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.840, 132.230, 167.420
Angle α, β, γ (deg.)90.000, 92.470, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules EJPR

#5: Protein
Pre-glycoprotein polyprotein GP complex / Pre-GP-C


Mass: 16425.861 Da / Num. of mol.: 4 / Fragment: UNP residues 87-228
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 , 4 types, 16 molecules AFKSBGLTCHMNDIOQ

#1: Antibody
CR1-28 Fab light chain


Mass: 22621.170 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: P0DOX7
#2: Antibody
CR1-28 Fab heavy chain


Mass: 24168.881 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: S6C4R2
#3: Antibody
CR1-10 Fab light chain


Mass: 23149.621 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: Q6PIL8
#4: Antibody
CR1-10 Fab heavy chain


Mass: 23785.506 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: S6B2B6

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Sugars , 3 types, 5 molecules

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


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#7: 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
#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.: 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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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: 3.89 Å3/Da / Density % sol: 68.35 %
Crystal growTemperature: 297 K / Method: batch mode / pH: 7.7 / Details: 1.9 M AmSO4 pH 7.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.99→49.35 Å / Num. obs: 57195 / % possible obs: 99.1 % / Redundancy: 3.401 % / Biso Wilson estimate: 22.23 Å2 / CC1/2: 0.796 / Rmerge(I) obs: 0.721 / Rrim(I) all: 0.857 / Χ2: 0.801 / Net I/σ(I): 2.34 / Num. measured all: 194531 / Scaling rejects: 78
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.99-4.233.4091.5861.0330534917789570.4651.88697.6
4.23-4.523.4211.0221.5729698870586800.6441.21699.7
4.52-4.883.4210.8131.8527660811480860.7390.96699.7
4.88-5.343.4130.7381.9725365745074320.770.87899.8
5.34-5.973.4070.8331.7823300686768380.7240.9999.6
5.97-6.873.3950.7961.8419914590258660.7320.94699.4
6.87-8.383.3550.4552.9117016511550720.9040.54199.2
8.38-11.683.370.1666.5513247397339310.9820.19898.9
11.68-49.353.3420.1347.537797240623330.9880.1697

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5EN2

5en2


Resolution: 3.99→49.35 Å / Cor.coef. Fo:Fc: 0.81 / Cor.coef. Fo:Fc free: 0.725 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.812
RfactorNum. reflection% reflectionSelection details
Rfree0.288 2860 5 %RANDOM
Rwork0.237 ---
obs0.239 57194 99.4 %-
Displacement parametersBiso max: 173 Å2 / Biso mean: 69 Å2 / Biso min: 22.14 Å2
Baniso -1Baniso -2Baniso -3
1--26.8976 Å20 Å2-2.9791 Å2
2--19.3767 Å20 Å2
3---7.5209 Å2
Refine analyzeLuzzati coordinate error obs: 0.78 Å
Refinement stepCycle: final / Resolution: 3.99→49.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30971 0 159 0 31130
Biso mean--35.02 --
Num. residues----4045
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d10551SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes5314HARMONIC5
X-RAY DIFFRACTIONt_it31962HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion4234SEMIHARMONIC5
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_contact33787SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d31962HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg43544HARMONIC21.15
X-RAY DIFFRACTIONt_omega_torsion2.41
X-RAY DIFFRACTIONt_other_torsion20.27
LS refinement shellResolution: 3.99→4.1 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2923 207 5.01 %
Rwork0.2366 3928 -
all0.2394 4135 -
obs--98.11 %

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