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- PDB-4jdt: Crystal structure of chimeric germ-line precursor of NIH45-46 Fab... -

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Basic information

Entry
Database: PDB / ID: 4jdt
TitleCrystal structure of chimeric germ-line precursor of NIH45-46 Fab in complex with gp120 of 93TH057 HIV-1
Components
  • Fab heavy chain
  • Fab light chain
  • gp120
Keywordsviral protein/immune system / IG FOLD / ANTI HIV / ANTIBODY / IMMUNE SYSTEM COMPLEX / 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 / molecular replacement / Resolution: 3.26 Å
AuthorsScharf, L. / Diskin, R. / Bjorkman, P.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural basis for HIV-1 gp120 recognition by a germ-line version of a broadly neutralizing antibody.
Authors: Scharf, L. / West, A.P. / Gao, H. / Lee, T. / Scheid, J.F. / Nussenzweig, M.C. / Bjorkman, P.J. / Diskin, R.
History
DepositionFeb 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / 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_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jun 2, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.gene_src_common_name ..._chem_comp.pdbx_synonyms / _entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_vector_type
Revision 1.4Sep 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 20, 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: gp120
H: Fab heavy chain
L: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7085
Polymers88,3913
Non-polymers3172
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.664, 69.815, 207.768
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein gp120


Mass: 40204.512 Da / Num. of mol.: 1 / Fragment: GP120 CORE / Mutation: UNP RESIDUES 43-122, 201-303, 325-486
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human Immunodeficiency Virus 1 / Strain: 93TH057 / Cell line (production host): Hi5 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q0ED31*PLUS
#2: Antibody Fab heavy chain


Mass: 25186.221 Da / Num. of mol.: 1 / Fragment: NIH45-46 Germ-line HEAVY CHAIN, IG GAMMA-1 CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human)
#3: Antibody Fab light chain


Mass: 23000.438 Da / Num. of mol.: 1 / Fragment: NIH45-46 LIGHT CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human)
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: 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 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
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: 2.69 Å3/Da / Density % sol: 54.34 %
Crystal growTemperature: 298 K / pH: 6.5
Details: PEG 10000, ammonium sulfate, Bis-Tris, isopropanol , pH 6.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.033
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2012
RadiationMonochromator: LIQUID NITROGEN-COOLED DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.256→29.711 Å / Num. obs: 15409 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.075
Reflection shellResolution: 3.26→3.43 Å / Rmerge(I) obs: 0.789 / % possible all: 91.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.43 Å29.71 Å
Translation7.43 Å29.71 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U7Y, 3U7W

3u7y

3u7w


Resolution: 3.26→29.71 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.4 / σ(F): 1.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.267 765 4.99 %
Rwork0.227 --
obs0.229 15346 98.3 %
all-15613 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 147.1 Å2
Refinement stepCycle: LAST / Resolution: 3.26→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5830 0 19 0 5849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016000
X-RAY DIFFRACTIONf_angle_d1.6428134
X-RAY DIFFRACTIONf_dihedral_angle_d13.2612162
X-RAY DIFFRACTIONf_chiral_restr0.077907
X-RAY DIFFRACTIONf_plane_restr0.011043
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2557-3.50680.31541360.28982717X-RAY DIFFRACTION93
3.5068-3.8590.35511570.26772905X-RAY DIFFRACTION100
3.859-4.41580.27161500.23192919X-RAY DIFFRACTION100
4.4158-5.55750.2431560.20572951X-RAY DIFFRACTION100
5.5575-29.71190.25311660.21773089X-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)
13.64640.77911.50323.81860.76387.5708-0.11410.68460.4232-1.0834-0.5464-0.23570.7861.37740.71371.9752-0.0481-0.20981.14960.25210.948712.019610.0278-50.535
26.67210.67782.00818.0432-0.45396.4790.4984-0.25280.5854-0.0091-1.419-0.40420.49831.13620.94641.2614-0.02440.06181.23410.19650.830313.27213.7611-38.3274
39.57465.2084-0.97313.40310.22690.01630.85930.0370.541-0.8254-0.33810.7668-0.6232-0.47480.04752.55310.3874-0.37281.44490.15191.0337-4.3332-6.5491-55.535
43.36772.3937-1.43786.0662-1.42887.0960.1-0.7757-0.53520.2872-1.0157-1.8984-0.92621.65110.83061.4069-0.1182-0.23171.35570.48871.315220.1838-0.9141-38.7511
57.98232.51012.22784.2728-0.54636.8065-0.83661.9683-2.8641-2.45890.6524-2.9326-1.71891.64011.81512.4095-0.13330.49020.97370.47951.533915.8938-18.1987-55.4896
65.40382.4801-2.22485.16050.83785.1215-0.65640.1605-0.8853-1.148-0.2574-1.0420.67510.8491.05331.87690.22140.46390.99750.30311.135813.4674-19.4078-47.6627
71.50070.8757-1.93943.00171.69895.159-1.019-0.3143-1.37670.1943-0.3229-1.02340.16720.8871.18851.05820.0980.03761.33870.68511.388515.086-10.4031-34.9854
84.91043.35540.8058.05271.00487.04460.15860.1096-0.0928-1.492-0.6628-0.2650.0284-0.61980.57431.12140.11530.08860.94350.01350.4999-2.5187-25.7134-27.0053
95.41941.92320.72818.87993.37235.64710.4629-1.18921.35990.0845-1.5367-0.0264-2.0186-1.32450.51891.8210.2279-0.13611.1759-0.10820.8503-2.1566-18.2695-19.9403
105.83291.1823-5.15047.19372.92359.5558-0.29410.77980.4038-0.5480.42230.4181-0.3686-0.5175-0.10260.82820.0213-0.03040.96320.12810.6405-19.5368-43.6386-1.0651
113.25910.5406-3.04162.6332-0.03453.4631-0.16791.23814.3303-0.2510.00821.7714-3.2033-2.12130.35350.9387-0.40880.0561.62730.37121.0339-28-46.4566-4.5089
127.52310.24772.09986.773-3.23653.2193-0.311-0.89210.3762.0502-0.7909-1.0032-0.92070.22380.80281.7139-0.4914-0.30211.22170.09620.87164.674-16.7885-5.5575
134.7679-5.4409-3.65868.0221.49147.53540.37341.2520.07862.0537-1.1154-1.5817-0.00571.7950.58472.4126-0.5357-0.83991.97370.40661.511612.1465-12.6091-3.4288
141.70530.2934-0.74344.3085-8.68976.61510.05970.82920.67482.3798-0.4971-0.8252-1.5133-1.30160.52161.669-0.3228-0.26731.3366-0.09160.98731.0732-22.3603-0.5173
155.08663.64342.16456.68170.78210.0144-0.1714-0.5769-0.39710.06230.0862-0.1706-0.35070.47490.08270.91390.04850.14151.08150.28480.9022-7.9816-49.35578.6456
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'G' and (resid 44 through 83 )
2X-RAY DIFFRACTION2chain 'G' and (resid 84 through 115 )
3X-RAY DIFFRACTION3chain 'G' and (resid 116 through 215 )
4X-RAY DIFFRACTION4chain 'G' and (resid 216 through 283 )
5X-RAY DIFFRACTION5chain 'G' and (resid 284 through 334 )
6X-RAY DIFFRACTION6chain 'G' and (resid 335 through 456 )
7X-RAY DIFFRACTION7chain 'G' and (resid 457 through 491 )
8X-RAY DIFFRACTION8chain 'H' and (resid 2 through 87 )
9X-RAY DIFFRACTION9chain 'H' and (resid 88 through 115 )
10X-RAY DIFFRACTION10chain 'H' and (resid 116 through 207 )
11X-RAY DIFFRACTION11chain 'H' and (resid 208 through 216 )
12X-RAY DIFFRACTION12chain 'L' and (resid 3 through 59 )
13X-RAY DIFFRACTION13chain 'L' and (resid 60 through 73 )
14X-RAY DIFFRACTION14chain 'L' and (resid 74 through 109 )
15X-RAY DIFFRACTION15chain 'L' and (resid 110 through 208 )

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