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- PDB-6urh: Crystal structure of broadly neutralizing antibody AR3X in comple... -

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Basic information

Entry
Database: PDB / ID: 6urh
TitleCrystal structure of broadly neutralizing antibody AR3X in complex with Hepatitis C virus envelope glycoprotein E2 ectodomain
Components
  • AR3X Heavy Chain
  • AR3X Light Chain
  • HCV envelope glycoprotein E2
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HCV glycoprotein / broadly neutralizing antibodies / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


virus-mediated perturbation of host defense response => GO:0019049 / host cell mitochondrial membrane / host cell lipid droplet / host cell mitochondrion / lipid droplet / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / ribonucleoprotein complex / viral envelope ...virus-mediated perturbation of host defense response => GO:0019049 / host cell mitochondrial membrane / host cell lipid droplet / host cell mitochondrion / lipid droplet / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / ribonucleoprotein complex / viral envelope / host cell nucleus / structural molecule activity / virion membrane / membrane / cytoplasm
Similarity search - Function
Hepatitis C virus, Core protein, C-terminal / Hepatitis C virus core protein / Hepatitis C virus, Non-structural protein E2/NS1 / Hepatitis C virus non-structural protein E2/NS1 / Hepatitis C virus, Envelope glycoprotein E1 / Hepatitis C virus envelope glycoprotein E1
Similarity search - Domain/homology
Core protein precursor / Genome polyprotein
Similarity search - Component
Biological speciesHepacivirus C
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsFlyak, A.I. / Bjorkman, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI127469 United States
CitationJournal: Elife / Year: 2020
Title: An ultralong CDRH2 in HCV neutralizing antibody demonstrates structural plasticity of antibodies against E2 glycoprotein.
Authors: Flyak, A.I. / Ruiz, S.E. / Salas, J. / Rho, S. / Bailey, J.R. / Bjorkman, P.J.
History
DepositionOct 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
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.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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: HCV envelope glycoprotein E2
H: AR3X Heavy Chain
L: AR3X Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1218
Polymers79,7433
Non-polymers3,3785
Water3,639202
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.730, 69.231, 176.699
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 , 2 types, 2 molecules CH

#1: Protein HCV envelope glycoprotein E2


Mass: 29116.686 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepacivirus C / Plasmid: pCMV / Production host: Homo sapiens (human) / Strain (production host): HEK293-6E / References: UniProt: A0A2P0NE21, UniProt: A0A2P0NE26*PLUS
#2: Protein AR3X Heavy Chain


Mass: 27450.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTT5 / Production host: Homo sapiens (human) / Strain (production host): HEK293-6E

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Antibody / Non-polymers , 2 types, 203 molecules L

#3: Antibody AR3X Light Chain


Mass: 23175.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTT5 / Production host: Homo sapiens (human) / Strain (production host): HEK293-6E
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 5 types, 5 molecules

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


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source
DescriptorTypeProgram
DManpa1-6DManpb1-3DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b3-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#7: 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-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.: 1 / Source method: isolated from a natural 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 ligand of interestN

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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: 2.48 Å3/Da / Density % sol: 50.45 % / Mosaicity: 0.46 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.25 M ammonium tartrate dibasic pH 7.0, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→64.73 Å / Num. obs: 40956 / % possible obs: 99.4 % / Redundancy: 6 % / Biso Wilson estimate: 44.39 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.05 / Rrim(I) all: 0.123 / Net I/σ(I): 9 / Num. measured all: 243765 / Scaling rejects: 194
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.4 / Num. measured all: 20579 / Num. unique obs: 3516 / CC1/2: 0.375 / Rpim(I) all: 0.626 / Rrim(I) all: 1.537 / Net I/σ(I) obs: 1.4 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.7.2data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
MOSFLM7.2.2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MWF, 6MEI

4mwf

6mei


Resolution: 2.2→54.493 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2325 1965 4.81 %
Rwork0.1865 38918 -
obs0.1887 40883 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 164.27 Å2 / Biso mean: 58.4741 Å2 / Biso min: 23.26 Å2
Refinement stepCycle: final / Resolution: 2.2→54.493 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4697 0 225 202 5124
Biso mean--99.77 51.72 -
Num. residues----616
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.2550.35831490.29842747100
2.255-2.3160.36731430.3115271398
2.316-2.38420.32951240.2788273799
2.3842-2.46110.31661300.25552734100
2.4611-2.54910.30841370.2412766100
2.5491-2.65110.29291430.232274599
2.6511-2.77180.28641210.22292798100
2.7718-2.91790.27161320.2152274499
2.9179-3.10070.29061380.21252773100
3.1007-3.34010.25011510.18912776100
3.3401-3.67620.20841610.1795275999
3.6762-4.20790.1761380.153279999
4.2079-5.30080.17121500.1294286499
5.3008-54.4930.22071480.1733296399
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)
19.15370.44072.4746.4570.00299.39620.025-0.6875-0.30590.32380.167-0.08970.2893-0.2681-0.14970.4377-0.18860.06490.53790.02430.3898-22.901-19.45526.463
25.6463-0.05650.293.0823-1.01452.7242-0.2415-0.6741-0.360.06070.0266-1.098-0.61831.29350.34040.7576-0.2899-0.00410.70220.12170.5345-12.891-13.28422.455
33.5477-0.59041.02413.443-0.28083.7675-0.28480.508-0.312-0.72880.2938-0.11670.3928-0.1342-0.00340.5912-0.28610.05410.5719-0.07230.4252-22.827-21.90912.244
46.46063.17741.12978.5971-2.73175.50780.03320.3115-0.5596-0.3179-0.1332-0.9558-0.00751.14060.08380.5767-0.32010.06980.7592-0.08260.5433-9.684-11.48113.313
54.12982.20864.76922.38722.40375.53770.24660.6370.5922-0.5456-0.1522-0.28461.1283-0.04490.03040.8837-0.27810.08060.7502-0.00240.541-12.178-4.091.278
68.92321.70891.8864.37252.7082.332-0.22710.69140.7104-0.2146-0.47750.0433-0.44260.56130.80110.6418-0.32250.03540.71170.03020.5375-12.515-4.1195.276
70.99530.34881.87922.20141.78617.2569-0.26990.2810.0102-0.34940.2758-0.049-0.35790.1955-0.00360.3604-0.05440.00620.4370.00110.3237-20.389-8.98648.502
83.78-2.91461.5526.4775-1.59023.0245-0.00930.038-0.06280.0457-0.1906-0.11580.03670.18360.21630.13270.0033-0.00030.30170.0050.3276-2.956-20.25280.771
92.20810.87320.75695.6765-1.77825.2532-0.04720.4916-0.404-0.76620.34570.17940.9144-0.3185-0.28650.5424-0.0843-0.07910.5126-0.12250.3947-24.821-29.40752.858
101.2861-0.0190.53534.13682.51846.8170.1039-0.1792-0.2970.0560.18830.03690.41590.0412-0.29640.15840.0303-0.06130.28830.03280.461-15.354-27.51587.549
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN C AND RESID 421:438 )C421 - 438
2X-RAY DIFFRACTION2( CHAIN C AND RESID 439:495 )C439 - 495
3X-RAY DIFFRACTION3( CHAIN C AND RESID 496:564 )C496 - 564
4X-RAY DIFFRACTION4( CHAIN C AND RESID 565:624 )C565 - 624
5X-RAY DIFFRACTION5( CHAIN C AND RESID 625:636 )C625 - 636
6X-RAY DIFFRACTION6( CHAIN C AND RESID 637:645 )C637 - 645
7X-RAY DIFFRACTION7( CHAIN H AND RESID 4:142 )H4 - 142
8X-RAY DIFFRACTION8( CHAIN H AND RESID 143:214 )H143 - 214
9X-RAY DIFFRACTION9( CHAIN L AND RESID 1:107 )L1 - 107
10X-RAY DIFFRACTION10( CHAIN L AND RESID 108:213 )L108 - 213

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