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- PDB-4jkp: Restricting HIV-1 Pathways for Escape using Rationally-Designed A... -

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Basic information

Entry
Database: PDB / ID: 4jkp
TitleRestricting HIV-1 Pathways for Escape using Rationally-Designed Anti-HIV-1 Antibodies
Components
  • Heavy chain of antibody 45-46M2
  • Light chain of antibody 45-46M2
  • gp120Envelope glycoprotein GP120
Keywordsviral protein/immune system / IgG / Antibody / gp120 / 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 / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / 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: 2.82 Å
AuthorsDiskin, R. / Bjorkman, P.J.
CitationJournal: J.Exp.Med. / Year: 2013
Title: Restricting HIV-1 pathways for escape using rationally designed anti-HIV-1 antibodies.
Authors: Diskin, R. / Klein, F. / Horwitz, J.A. / Halper-Stromberg, A. / Sather, D.N. / Marcovecchio, P.M. / Lee, T. / West, A.P. / Gao, H. / Seaman, M.S. / Stamatatos, L. / Nussenzweig, M.C. / Bjorkman, P.J.
History
DepositionMar 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: gp120
H: Heavy chain of antibody 45-46M2
L: Light chain of antibody 45-46M2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,17611
Polymers88,5003
Non-polymers3,6768
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11390 Å2
ΔGint52 kcal/mol
Surface area35100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.330, 70.490, 232.220
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 45-46M2


Mass: 25218.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Antibody Light chain of antibody 45-46M2


Mass: 23076.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

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Protein / Non-polymers , 2 types, 24 molecules G

#1: Protein gp120 / Envelope glycoprotein GP120


Mass: 40204.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q0ED31*PLUS
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 4 types, 8 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...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: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e6-f1WURCSPDB2Glycan 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]{[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[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: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 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]{}}}}}LINUCSPDB-CARE
#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.: 1
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: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 12% (v/v) isopropanol, 10% (w/v) polyethylene glycol 10,000 kD, 0.1 M citrate , pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2012
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.82→34.85 Å / Num. all: 28298 / Num. obs: 27846 / % possible obs: 98.4 % / Observed criterion σ(F): 999999 / Observed criterion σ(I): 999999
Reflection shellResolution: 2.82→2.89 Å / % possible all: 99.3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: dev_1026)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.82→34.846 Å / SU ML: 0.35 / σ(F): 1.35 / Phase error: 25.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.231 1390 4.99 %
Rwork0.1934 --
obs0.1953 27838 98.46 %
all-28298 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.82→34.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5987 0 242 23 6252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076397
X-RAY DIFFRACTIONf_angle_d1.0278674
X-RAY DIFFRACTIONf_dihedral_angle_d12.9922366
X-RAY DIFFRACTIONf_chiral_restr0.064995
X-RAY DIFFRACTIONf_plane_restr0.0141091
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.82-2.92070.33311370.29972615X-RAY DIFFRACTION99
2.9207-3.03760.36681340.28512591X-RAY DIFFRACTION99
3.0376-3.17580.33331430.25652626X-RAY DIFFRACTION99
3.1758-3.34310.30371360.22792601X-RAY DIFFRACTION99
3.3431-3.55240.25141350.21272647X-RAY DIFFRACTION99
3.5524-3.82630.22881340.1872641X-RAY DIFFRACTION99
3.8263-4.21080.23531400.1712621X-RAY DIFFRACTION99
4.2108-4.81870.1531410.13942639X-RAY DIFFRACTION98
4.8187-6.06590.191390.16642686X-RAY DIFFRACTION98
6.0659-34.84860.22141510.20472781X-RAY DIFFRACTION97
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)
11.23781.0613-0.27041.88410.9511.9362-0.0617-0.14580.27240.13930.19590.0426-0.13140.1784-0.10680.54680.1808-0.05860.4964-0.0110.631946.405134.33724.3199
24.2583-0.90940.18041.14280.47213.3837-0.2059-0.187-0.18760.3280.03530.09680.0971-0.3150.11570.3339-0.03320.03580.38120.02110.442354.735627.78034.4416
33.4538-0.98780.13462.21530.84734.1661-0.1313-0.02970.3181-0.00770.06790.0085-0.18430.31940.05270.3461-0.0989-0.02180.34790.04990.467373.765632.53162.4748
43.12240.6671-0.54031.9418-1.01921.9243-0.1089-0.46120.373-0.0167-0.02570.2236-0.2071-0.06170.18010.43350.0095-0.02660.2889-0.11090.417565.691434.771811.0814
54.49982.0763-0.64532.37-0.30610.09610.0356-1.74480.17141.5316-0.27160.6143-1.3991-0.1696-0.05510.96430.4639-0.03021.0654-0.32270.568474.300533.076550.8732
62.2033-0.19090.25540.60061.17982.3427-0.5305-1.58710.39320.71230.50290.5134-0.3048-1.04080.10070.80890.43320.0331.3898-0.0710.588267.905628.561244.1876
70.31940.60810.83050.58020.88881.5515-0.3962-1.25480.34920.33630.23290.3683-0.6438-0.3716-0.58780.68080.33590.06191.6002-0.09040.257278.261925.957953.4416
83.58770.32090.19562.82620.61034.23360.0486-0.1707-0.02770.4375-0.0477-0.302-0.3229-0.41760.04590.73010.075-0.14460.6790.06640.5275100.415816.957464.5702
92.5524-1.94740.50214.0473-0.00014.5726-0.1177-0.4291-0.06680.19630.03360.14920.1203-0.24860.09040.31590.01250.01390.56480.02470.350777.609418.846526.6614
101.81550.52330.94292.4777-1.57968.1559-0.2121-0.0478-0.31440.374-0.621-0.0790.41970.43760.75920.68530.0275-0.160.5428-0.04360.56899.79245.943355.8214
112.7284-0.9187-0.2871.79420.18212.64390.14740.0414-0.377-0.1691-0.2148-0.02020.6843-0.26670.09930.6655-0.0159-0.12110.5820.03370.640794.37592.330756.982
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'G' and (resid 44 through 98 )
2X-RAY DIFFRACTION2chain 'G' and (resid 99 through 258 )
3X-RAY DIFFRACTION3chain 'G' and (resid 259 through 442 )
4X-RAY DIFFRACTION4chain 'G' and (resid 443 through 492 )
5X-RAY DIFFRACTION5chain 'L' and (resid 3 through 24 )
6X-RAY DIFFRACTION6chain 'L' and (resid 25 through 88 )
7X-RAY DIFFRACTION7chain 'L' and (resid 89 through 109 )
8X-RAY DIFFRACTION8chain 'L' and (resid 110 through 209 )
9X-RAY DIFFRACTION9chain 'H' and (resid 2 through 115 )
10X-RAY DIFFRACTION10chain 'H' and (resid 116 through 149 )
11X-RAY DIFFRACTION11chain 'H' and (resid 150 through 218 )

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