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- PDB-4jpw: Crystal structure of broadly and potently neutralizing antibody 1... -

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Basic information

Entry
Database: PDB / ID: 4jpw
TitleCrystal structure of broadly and potently neutralizing antibody 12a21 in complex with hiv-1 strain 93th057 gp120 mutant
Components
  • HEAVY CHAIN OF ANTIBODY 12A21
  • HIV-1 CLADE A/E STRAIN 73TH057 GP120 WITH MUTATION H375S
  • LIGHT CHAIN OF ANTIBODY 12A21
Keywordsviral protein/immune system / HIV / GP120 / CD4-BINDING SITE / 12A21 / 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 / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / 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 ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / 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 / plasma 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: 2.904 Å
AuthorsAcharya, P. / Luongo, T. / Zhou, T. / Kwong, P.D.
Citation
Journal: 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.
#1: Journal: Immunity / Year: 2013
Title: Multidonor Analysis Reveals Structural Elements, Genetic Determinants, and Maturation Pathway for HIV-1 Neutralization by VRC01-Class Antibodies.
Authors: Zhou, T. / Zhu, J. / Wu, X. / Moquin, S. / Zhang, B. / Acharya, P. / Georgiev, I.S. / Altae-Tran, H.R. / Chuang, G.Y. / Joyce, M.G. / Do Kwon, Y. / Longo, N.S. / Louder, M.K. / Luongo, T. / ...Authors: Zhou, T. / Zhu, J. / Wu, X. / Moquin, S. / Zhang, B. / Acharya, P. / Georgiev, I.S. / Altae-Tran, H.R. / Chuang, G.Y. / Joyce, M.G. / Do Kwon, Y. / Longo, N.S. / Louder, M.K. / Luongo, T. / McKee, K. / Schramm, C.A. / Skinner, J. / Yang, Y. / Yang, Z. / Zhang, Z. / Zheng, A. / Bonsignori, M. / Haynes, B.F. / Scheid, J.F. / Nussenzweig, M.C. / Simek, M. / Burton, D.R. / Koff, W.C. / Mullikin, J.C. / Connors, M. / Shapiro, L. / Nabel, G.J. / Mascola, J.R. / Kwong, P.D.
History
DepositionMar 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Jul 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 1.3Sep 20, 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: HIV-1 CLADE A/E STRAIN 73TH057 GP120 WITH MUTATION H375S
H: HEAVY CHAIN OF ANTIBODY 12A21
L: LIGHT CHAIN OF ANTIBODY 12A21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,91314
Polymers86,4623
Non-polymers2,45011
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9280 Å2
ΔGint21 kcal/mol
Surface area34560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.975, 65.987, 213.023
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 12A21


Mass: 24411.502 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 12A21


Mass: 22890.564 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, 11 molecules G

#1: Protein HIV-1 CLADE A/E STRAIN 73TH057 GP120 WITH MUTATION H375S


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 / 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10
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, 63 molecules

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


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 10% PEG 4000, 0.5% isopropanol, 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-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 22, 2012
RadiationMonochromator: APS 22ID / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 20065 / Num. obs: 19490 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.08 / Rsym value: 0.1 / Net I/σ(I): 11
Reflection shellResolution: 2.85→2.88 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2 / Rsym value: 0.48 / % possible all: 86.3

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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: 2.904→41.443 Å / SU ML: 0.41 / σ(F): 1.37 / Phase error: 27.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2653 987 5.06 %Radom
Rwork0.2063 ---
obs0.2092 19490 97.13 %-
all-20065 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.916 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-14.452 Å2-0 Å2-0 Å2
2---4.167 Å2-0 Å2
3----10.285 Å2
Refinement stepCycle: LAST / Resolution: 2.904→41.443 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5994 0 155 62 6211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026309
X-RAY DIFFRACTIONf_angle_d0.5968562
X-RAY DIFFRACTIONf_dihedral_angle_d12.3872315
X-RAY DIFFRACTIONf_chiral_restr0.038973
X-RAY DIFFRACTIONf_plane_restr0.0031085
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9036-3.05670.36051270.30392270X-RAY DIFFRACTION85
3.0567-3.24810.37061420.26182574X-RAY DIFFRACTION96
3.2481-3.49880.29251400.24422670X-RAY DIFFRACTION99
3.4988-3.85070.29391550.21042678X-RAY DIFFRACTION100
3.8507-4.40730.22221320.18142725X-RAY DIFFRACTION100
4.4073-5.55070.22091580.16292726X-RAY DIFFRACTION100
5.5507-41.44680.24671330.20412860X-RAY DIFFRACTION99
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)
15.5920.8442-3.33595.8136-0.78585.7252-0.1665-0.1592-0.47-0.06570.10580.21560.4521-0.29720.0790.48840.0637-0.12930.35290.01660.3873-13.6236-30.6349-44.086
24.00520.0307-2.06563.5865-0.24155.443-0.04560.03230.2326-0.40580.11660.4438-0.1787-0.391-0.0590.45470.0389-0.14160.2844-0.00510.461-15.2822-7.8367-47.1414
34.23422.4691.46714.79551.66263.78430.2711-0.30230.07510.5298-0.3292-0.1057-0.31680.15410.0390.4801-0.0634-0.02470.41240.06640.30664.691-3.3129-27.3918
46.677-1.20721.60447.5773-1.08532.392-0.0381-0.37460.25640.34240.0384-0.4507-0.0350.4441-0.02310.4615-0.02250.02020.5603-0.10210.341325.67777.3985-0.8815
56.78691.59090.76693.54360.62235.68510.0916-0.5760.14790.6417-0.2418-0.1066-0.0304-0.10780.16710.66140.00290.00170.3643-0.00270.3121-3.6346-14.5348-8.7605
62.8862.55131.00656.94940.85832.8640.0034-0.33650.39140.3156-0.03820.421-0.1942-0.0570.02130.40380.05770.00090.4797-0.06690.384612.16910.05367.2485
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 1:118
4X-RAY DIFFRACTION4chain H and resid 119:217
5X-RAY DIFFRACTION5chain L and resid 1:97
6X-RAY DIFFRACTION6chain L and resid 98:214

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