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- PDB-4jpk: Crystal structure of the germline-targeting HIV-1 gp120 engineere... -

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Basic information

Entry
Database: PDB / ID: 4jpk
TitleCrystal structure of the germline-targeting HIV-1 gp120 engineered outer domain eOD-GT6 in complex with a putative VRC01 germline precursor Fab
Components
  • Germline-targeting HIV-1 gp120 engineered outer domain, eOD-GT6
  • Putative VRC01 germline precursor Fab heavy chain
  • Putative VRC01 germline precursor Fab light chain
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / HIV-1 gp120 / CD4 binding / VRC01-like broadly neutralizing antibodies / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / 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 ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / 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 / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / 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
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsJulien, J.-P. / Jardine, J. / Schief, W.R. / Wilson, I.A.
CitationJournal: Science / Year: 2013
Title: Rational HIV immunogen design to target specific germline B cell receptors.
Authors: Jardine, J. / Julien, J.P. / Menis, S. / Ota, T. / Kalyuzhniy, O. / McGuire, A. / Sok, D. / Huang, P.S. / MacPherson, S. / Jones, M. / Nieusma, T. / Mathison, J. / Baker, D. / Ward, A.B. / ...Authors: Jardine, J. / Julien, J.P. / Menis, S. / Ota, T. / Kalyuzhniy, O. / McGuire, A. / Sok, D. / Huang, P.S. / MacPherson, S. / Jones, M. / Nieusma, T. / Mathison, J. / Baker, D. / Ward, A.B. / Burton, D.R. / Stamatatos, L. / Nemazee, D. / Wilson, I.A. / Schief, W.R.
History
DepositionMar 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Jan 15, 2014Group: Source and taxonomy
Revision 1.3Jul 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_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 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
H: Putative VRC01 germline precursor Fab heavy chain
L: Putative VRC01 germline precursor Fab light chain
A: Germline-targeting HIV-1 gp120 engineered outer domain, eOD-GT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5965
Polymers68,1543
Non-polymers4422
Water3,117173
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)179.260, 63.300, 61.300
Angle α, β, γ (deg.)90.00, 90.43, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-310-

HOH

21A-347-

HOH

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Components

#1: Antibody Putative VRC01 germline precursor Fab heavy chain


Mass: 26541.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody Putative VRC01 germline precursor Fab light chain


Mass: 23035.514 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein Germline-targeting HIV-1 gp120 engineered outer domain, eOD-GT6


Mass: 18576.861 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Cell line (production host): HEK 293S / Production host: Homo sapiens (human) / References: UniProt: P04578*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.: 2
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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.55 Å3/Da / Density % sol: 51.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 20% w/v PEG4000, 0.1 M sodium citrate, 20% v/v 2-propanol, pH 5.6, 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: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 22, 2012
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. all: 27113 / Num. obs: 25368 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rsym value: 0.085 / Net I/σ(I): 9.4
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.432 / % possible all: 96.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 4JPI AND 4JPJ

4jpi

4jpj


Resolution: 2.4→36.307 Å / SU ML: 0.33 / σ(F): 1.34 / Phase error: 29.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1253 4.95 %RANDOM
Rwork0.2 ---
obs0.203 25311 93.38 %-
all-27113 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→36.307 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4560 0 28 173 4761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054702
X-RAY DIFFRACTIONf_angle_d0.9686379
X-RAY DIFFRACTIONf_dihedral_angle_d14.9351685
X-RAY DIFFRACTIONf_chiral_restr0.064716
X-RAY DIFFRACTIONf_plane_restr0.004821
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.4960.31991360.27122749X-RAY DIFFRACTION96
2.496-2.60960.41671470.27612715X-RAY DIFFRACTION96
2.6096-2.74710.36641290.29892498X-RAY DIFFRACTION87
2.7471-2.91920.26671380.2312686X-RAY DIFFRACTION95
2.9192-3.14440.26711480.20372808X-RAY DIFFRACTION98
3.1444-3.46070.2541360.19712633X-RAY DIFFRACTION93
3.4607-3.96090.26691350.19362495X-RAY DIFFRACTION87
3.9609-4.98830.21541430.15882707X-RAY DIFFRACTION94
4.9883-36.31110.24311410.18342767X-RAY DIFFRACTION94
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)
13.6473-1.5604-0.54754.2753-2.32021.8594-0.42640.31810.5995-0.2213-0.4835-0.0812-0.93830.67130.77090.16780.01180.0330.41640.05870.2994-12.61579.118.0767
23.4236-1.13240.60354.50581.00170.820.0322-0.27910.32930.3531-0.3572-0.6265-0.54620.0150.16230.2333-0.094-0.00550.4910.07760.3171-2.94084.89317.0035
36.0385-2.9812-3.30273.95410.73042.77430.20080.0265-0.293-0.0085-0.01470.3785-0.0955-0.1304-0.16810.2486-0.03260.01050.36620.11690.2565-11.3705-2.94614.039
42.8371-1.1285-1.3883.6341-0.58441.22190.01220.035-0.0877-0.182-0.1425-0.208-0.1184-0.15220.09620.22860.0285-0.00610.40780.00410.2643-10.1799-0.978511.7685
51.708-1.46421.50871.6374-0.90571.94490.0753-0.1635-0.12910.0375-0.0640.43380.0238-0.25310.00670.2126-0.02460.05330.3453-0.00430.4371-34.553415.93627.3249
64.60920.4328-0.51574.18680.95855.21540.2088-0.63280.27530.2361-0.0978-0.1761-0.1464-0.0594-0.12010.29050.0813-0.05850.43970.00980.2662-37.607720.27999.1599
77.4775-3.7025-0.1777.29291.00095.4440.2679-0.12151.7518-0.140.1536-0.3559-0.6513-0.4615-0.37130.30350.07390.04830.3387-0.00290.6628-38.169129.29034.4797
84.20960.2891-0.54922.10590.60586.6626-0.0762-0.5217-0.32720.40360.15090.1260.0325-0.26370.00480.2650.06890.03610.56960.10290.2966-23.4816-1.72430.7283
92.6757-0.67281.2430.8061-0.17941.2898-0.1649-0.6448-0.07810.24420.26470.1783-0.165-0.2488-0.05520.25560.04930.06780.49380.02610.3662-35.86946.187521.3397
104.04340.54231.47631.56930.94885.29980.0205-0.3384-0.43610.0646-0.02510.29590.16990.0942-0.01440.25690.03830.01660.38850.05550.4419-50.61288.88378.9028
114.63120.2687-0.47542.5057-0.36981.89680.221-0.0083-0.15580.11510.0575-0.4926-0.0037-0.0718-0.21590.2199-0.01-0.02520.2850.050.331711.9327-22.30878.0886
126.9453-4.791-4.53568.47550.27694.59660.13130.9573-0.7699-0.16250.30341.4190.7384-1.4461-0.25860.402-0.07250.03630.52860.00990.5168-12.0949-18.76111.5401
137.10961.01832.04114.9704-0.26799.75640.3961-0.3169-0.50440.1354-0.12230.5371-0.0828-0.1442-0.15740.256-0.03220.03160.58110.07110.32075.2848-11.855421.3696
148.86112.8663-0.12434.90280.34237.9278-0.122-0.7655-0.87360.70090.0394-0.15220.25830.3601-0.28850.3671-0.0044-0.0410.51910.0890.398411.2122-18.723320.0239
153.68181.73-0.48184.55251.0481.9925-0.3785-0.5742-0.59780.6986-0.0121-0.04210.7682-0.13130.52440.44460.07020.09350.62270.31420.73938.0521-29.314820.7076
162.23-2.61020.91868.7888-1.65522.7001-0.3132-0.59490.08540.36640.37260.70480.6148-0.0223-0.15880.39520.06060.00590.56880.1140.2791-5.1603-18.308323.9221
172.7251.17410.47563.3601-1.85711.62190.3096-0.1783-0.6194-0.27310.1581-0.27940.34230.0101-0.20810.31040.01610.09520.3245-0.03050.286410.8534-27.080412.3228
183.6095-1.5409-0.1183.51913.08354.3036-0.00970.1222-0.54720.3624-0.09430.15910.4334-0.25040.05940.2355-0.0379-0.00320.32940.120.4827-1.73-26.475310.6675
193.8691-1.79033.00976.41070.21387.24350.66950.28751.1185-0.3304-0.0398-0.7028-0.43130.5468-0.29620.304-0.05760.1330.3213-0.01210.365412.362-13.551110.4789
205.0247-2.22814.91766.06260.24225.95960.6250.88211.0351-0.2421-0.2447-0.9649-0.9561.612-0.32910.3744-0.12450.08250.73720.13790.549418.663-13.52338.8913
215.28784.8443-3.57444.4024-2.64155.5890.32811.1201-0.43810.4079-0.1413-0.09150.14060.063-0.0670.22340.0166-0.04580.3539-0.00350.3201-0.9356-24.62734.9367
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 17 )
2X-RAY DIFFRACTION2chain 'H' and (resid 18 through 33 )
3X-RAY DIFFRACTION3chain 'H' and (resid 34 through 56 )
4X-RAY DIFFRACTION4chain 'H' and (resid 57 through 100 )
5X-RAY DIFFRACTION5chain 'H' and (resid 101 through 145 )
6X-RAY DIFFRACTION6chain 'H' and (resid 146 through 188 )
7X-RAY DIFFRACTION7chain 'H' and (resid 189 through 213 )
8X-RAY DIFFRACTION8chain 'L' and (resid 1 through 61 )
9X-RAY DIFFRACTION9chain 'L' and (resid 62 through 142 )
10X-RAY DIFFRACTION10chain 'L' and (resid 143 through 214 )
11X-RAY DIFFRACTION11chain 'A' and (resid 1 through 26 )
12X-RAY DIFFRACTION12chain 'A' and (resid 27 through 40 )
13X-RAY DIFFRACTION13chain 'A' and (resid 41 through 50 )
14X-RAY DIFFRACTION14chain 'A' and (resid 51 through 61 )
15X-RAY DIFFRACTION15chain 'A' and (resid 62 through 73 )
16X-RAY DIFFRACTION16chain 'A' and (resid 74 through 86 )
17X-RAY DIFFRACTION17chain 'A' and (resid 87 through 103 )
18X-RAY DIFFRACTION18chain 'A' and (resid 104 through 141 )
19X-RAY DIFFRACTION19chain 'A' and (resid 142 through 151 )
20X-RAY DIFFRACTION20chain 'A' and (resid 152 through 158 )
21X-RAY DIFFRACTION21chain 'A' and (resid 159 through 169 )

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