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- PDB-4jpv: Crystal structure of broadly and potently neutralizing antibody 3... -

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Basic information

Entry
Database: PDB / ID: 4jpv
TitleCrystal structure of broadly and potently neutralizing antibody 3bnc117 in complex with hiv-1 gp120
Components
  • HEAVY CHAIN OF ANTIBODY 3BNC117
  • HIV-1 CLADE A STRAIN 93TH057 GP120 WITH LOOP d AND LOOPD V5 REPLACED FROM HIV STRAIN 3415V1
  • LIGHT CHAIN OF ANTIBODY 3BNC117
Keywordsviral protein/immune system / HIV / GP120 / CD4-BINDING SITE / 3BNC117 / NEUTRALIZATION / VACCINE / ANTIBODY / ENVELOPE PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Beta Complex / Immunoglobulins ...HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Beta Complex / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.827 Å
AuthorsZhou, T. / Moquin, S. / Kwong, P.D.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2013
Title: Somatic Mutations of the Immunoglobulin Framework Are Generally Required for Broad and Potent HIV-1 Neutralization.
Authors: Klein, F. / Diskin, R. / Scheid, J.F. / Gaebler, C. / Mouquet, H. / Georgiev, I.S. / Pancera, M. / Zhou, T. / Incesu, R.B. / Fu, B.Z. / Gnanapragasam, P.N. / Oliveira, T.Y. / Seaman, M.S. / ...Authors: Klein, F. / Diskin, R. / Scheid, J.F. / Gaebler, C. / Mouquet, H. / Georgiev, I.S. / Pancera, M. / Zhou, T. / Incesu, R.B. / Fu, B.Z. / Gnanapragasam, P.N. / Oliveira, T.Y. / Seaman, M.S. / Kwong, P.D. / Bjorkman, P.J. / Nussenzweig, M.C.
History
DepositionMar 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jun 2, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 9, 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
G: HIV-1 CLADE A STRAIN 93TH057 GP120 WITH LOOP d AND LOOPD V5 REPLACED FROM HIV STRAIN 3415V1
H: HEAVY CHAIN OF ANTIBODY 3BNC117
L: LIGHT CHAIN OF ANTIBODY 3BNC117
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,78119
Polymers86,8623
Non-polymers2,92016
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9820 Å2
ΔGint40 kcal/mol
Surface area36180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.627, 69.887, 231.633
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 HEAVY CHAIN OF ANTIBODY 3BNC117


Mass: 24656.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: HOMO SAPIENS (human)
#3: Antibody LIGHT CHAIN OF ANTIBODY 3BNC117


Mass: 23022.658 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: HOMO SAPIENS (human)

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Protein / Sugars , 2 types, 12 molecules G

#1: Protein HIV-1 CLADE A STRAIN 93TH057 GP120 WITH LOOP d AND LOOPD V5 REPLACED FROM HIV STRAIN 3415V1


Mass: 39182.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 / Cell line (production host): HEK293F / Production host: HOMO SAPIENS (human) / References: UniProt: Q0ED31*PLUS
#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


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 , 3 types, 86 molecules

#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 3.2 Å3/Da / Density % sol: 61.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, 11% PEG 8000, 7% ethylene glycol , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorDetector: CCD / Date: Dec 5, 2011
RadiationMonochromator: APS 22-BM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 27456 / Num. obs: 27017 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 14.1
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.62 / % possible all: 87.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: dev_998)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SE9

3se9


Resolution: 2.827→48.966 Å / SU ML: 0.4 / σ(F): 1.35 / Phase error: 28.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2593 1371 5.09 %RANDOM
Rwork0.1994 ---
obs0.2025 26952 97.9 %-
all-27530 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.806 Å2 / ksol: 0.353 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.463 Å2-0 Å20 Å2
2---6.7008 Å20 Å2
3---16.1638 Å2
Refinement stepCycle: LAST / Resolution: 2.827→48.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5958 0 185 81 6224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046306
X-RAY DIFFRACTIONf_angle_d0.8768555
X-RAY DIFFRACTIONf_dihedral_angle_d13.2482320
X-RAY DIFFRACTIONf_chiral_restr0.059963
X-RAY DIFFRACTIONf_plane_restr0.0051084
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8269-2.9280.42311230.33072228X-RAY DIFFRACTION87
2.928-3.04520.28591240.25862528X-RAY DIFFRACTION98
3.0452-3.18370.30281290.22552570X-RAY DIFFRACTION100
3.1837-3.35160.27161340.21752562X-RAY DIFFRACTION100
3.3516-3.56150.26551440.20782569X-RAY DIFFRACTION100
3.5615-3.83640.23441360.18222571X-RAY DIFFRACTION99
3.8364-4.22220.23371360.17162574X-RAY DIFFRACTION99
4.2222-4.83280.23171570.15742576X-RAY DIFFRACTION99
4.8328-6.08690.23411420.18532610X-RAY DIFFRACTION98
6.0869-48.97330.28261460.21882793X-RAY DIFFRACTION100
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)
13.1961.53291.32654.01151.83912.99150.1260.0584-0.2150.0802-0.1460.34270.2966-0.21780.02650.38460.0450.03980.35740.00350.9685-19.09433.3739-6.1982
22.79580.344-0.07542.60841.1363.6291-0.01860.1066-0.68560.112-0.012-0.19330.4160.3410.01680.44180.05870.04630.36640.02160.99353.3976-1.1781-6.2006
39.29071.2425-1.31996.2802-2.49876.19670.17040.58260.5133-0.198-0.02730.4892-0.2090.2578-0.12420.3869-0.0386-0.03780.509-0.03990.44159.098315.3018-27.8491
43.61210.33790.71633.388-2.09884.70910.231-0.14380.3578-0.37610.1478-0.1122-0.7869-1.2802-0.36110.94540.36290.28911.3180.23770.844626.555929.3566-55.0503
53.8221-0.95160.37824.1783-0.35247.1436-0.33892.08220.1166-1.02920.03420.56090.3821-0.45570.23490.7606-0.1432-0.22581.4393-0.0170.8175-1.91797.8003-47.6586
65.87162.32350.74283.80690.26672.8038-0.57980.6931-0.8154-0.96350.5483-0.38320.1493-0.24940.02711.0952-0.13420.22521.36350.08350.801228.857815.876-65.1678
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain G and (resid 44:253 or resid 476:492)
2X-RAY DIFFRACTION2chain G and resid 254:475
3X-RAY DIFFRACTION3chain H and resid 1:113
4X-RAY DIFFRACTION4chain H and resid 114:217
5X-RAY DIFFRACTION5chain L and resid 1:108
6X-RAY DIFFRACTION6chain L and resid 109:213

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