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- PDB-6bck: Crystal Structure of Broadly Neutralizing Antibody N49P7 in Compl... -

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Basic information

Entry
Database: PDB / ID: 6bck
TitleCrystal Structure of Broadly Neutralizing Antibody N49P7 in Complex with HIV-1 Clade AE strain 93TH057 gp120 core.
Components
  • N49P7 Fab heavy chain of N29P7 IgG
  • N49P7 Fab light chain from N49P7 IgG
  • clade A/E 93TH057 HIV-1 gp120 core
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HIV-1 / VRC01-CLASS ANTIBODY / CD4 binding site / CLADE A/E 93TH057 gp120 / viral protein-immune system complex / N49P7 / IMMUNE SYSTEM
Function / homologyGp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / viral envelope / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / clade A/E 93TH057 HIV-1 gp120 core
Function and homology information
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsTolbert, W.D. / Gohain, N. / Pazgier, M.
Funding support United States, 3items
OrganizationGrant numberCountry
VA Merit Review AwardVAIBX002358 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI110259 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI129769 United States
CitationJournal: Cell / Year: 2018
Title: Identification of Near-Pan-neutralizing Antibodies against HIV-1 by Deconvolution of Plasma Humoral Responses.
Authors: Sajadi, M.M. / Dashti, A. / Rikhtegaran Tehrani, Z. / Tolbert, W.D. / Seaman, M.S. / Ouyang, X. / Gohain, N. / Pazgier, M. / Kim, D. / Cavet, G. / Yared, J. / Redfield, R.R. / Lewis, G.K. / DeVico, A.L.
History
DepositionOct 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: clade A/E 93TH057 HIV-1 gp120 core
H: N49P7 Fab heavy chain of N29P7 IgG
L: N49P7 Fab light chain from N49P7 IgG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,35116
Polymers85,6813
Non-polymers2,67013
Water48627
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9130 Å2
ΔGint3 kcal/mol
Surface area34470 Å2
Unit cell
Length a, b, c (Å)61.436, 63.867, 255.285
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 2 molecules HL

#2: Antibody N49P7 Fab heavy chain of N29P7 IgG


Mass: 24757.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#3: Antibody N49P7 Fab light chain from N49P7 IgG


Mass: 21763.061 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 12 molecules G

#1: Protein clade A/E 93TH057 HIV-1 gp120 core


Mass: 39160.367 Da / Num. of mol.: 1 / Mutation: H375S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: HIV-1 Env / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: A0A0M3KKW9
#4: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 11
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, 29 molecules

#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.92 Å3/Da / Density % sol: 57.92 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 10% PEG 5000 MME 12% isopropanol 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: May 31, 2017 / Details: RH coated flat mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.69→44.261 Å / Num. obs: 23639 / % possible obs: 80.6 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 9.3
Reflection shellResolution: 2.69→2.74 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.749 / Mean I/σ(I) obs: 1.07 / % possible all: 72.2

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TGT, 3TNN

3tgt

3tnn


Resolution: 2.7→44.261 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 31.41
RfactorNum. reflection% reflectionSelection details
Rfree0.2847 919 5.1 %Random selection
Rwork0.2248 ---
obs0.228 18015 63.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→44.261 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5822 0 170 27 6019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0146151
X-RAY DIFFRACTIONf_angle_d1.1638395
X-RAY DIFFRACTIONf_dihedral_angle_d8.463622
X-RAY DIFFRACTIONf_chiral_restr0.076964
X-RAY DIFFRACTIONf_plane_restr0.0091069
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.84240.4211560.35531220X-RAY DIFFRACTION32
2.8424-3.02040.3967820.32431627X-RAY DIFFRACTION43
3.0204-3.25350.35361110.26042059X-RAY DIFFRACTION54
3.2535-3.58080.29781450.24522599X-RAY DIFFRACTION68
3.5808-4.09870.30521770.21193181X-RAY DIFFRACTION83
4.0987-5.16260.22341760.18913167X-RAY DIFFRACTION81
5.1626-44.2670.26561720.21783243X-RAY DIFFRACTION79
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)
10.0304-0.00570.00960.0492-0.0019-0.0313-0.0680.1432-0.0340.05220.0051-0.26270.0037-0.18710-0.58670.1309-0.1417-0.2717-0.03940.2142-16.12695.9501-56.5601
2-0.03790.0224-0.0246-0.0323-0.03350.0009-0.04350.06290.03480.1198-0.1183-0.04220.0918-0.0392-00.07360.06260.4950.1329-0.0817-0.7795-39.5219-18.2398-25.3278
3-0.01710.0242-0.00890.0034-0.01210.0279-0.1141-0.0204-0.28860.06280.050.081-0.047-0.0216-00.61850.13930.09780.3297-0.03180.157-29.983-14.2121-11.959
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'G' and resid 44 through 491)
2X-RAY DIFFRACTION2(chain 'H' and resid 2 through 212)
3X-RAY DIFFRACTION3(chain 'L' and resid 3 through 208)

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