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

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Entry
Database: PDB / ID: 4jpj
TitleCrystal structure of the germline-targeting HIV-1 gp120 engineered outer domain, eOD-GT6
ComponentsGermline-targeting HIV-1 gp120 engineered outer domain, eOD-GT6
KeywordsVIRAL PROTEIN / HIV-1 gp120 / CD4 binding site / VRC01-like broadly neutralizing antibodies
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
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
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

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Assembly

Deposited unit
A: Germline-targeting HIV-1 gp120 engineered outer domain, eOD-GT6
B: Germline-targeting HIV-1 gp120 engineered outer domain, eOD-GT6
C: Germline-targeting HIV-1 gp120 engineered outer domain, eOD-GT6
D: Germline-targeting HIV-1 gp120 engineered outer domain, eOD-GT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,77412
Polymers80,0054
Non-polymers1,7708
Water81145
1
A: Germline-targeting HIV-1 gp120 engineered outer domain, eOD-GT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4443
Polymers20,0011
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Germline-targeting HIV-1 gp120 engineered outer domain, eOD-GT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4443
Polymers20,0011
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Germline-targeting HIV-1 gp120 engineered outer domain, eOD-GT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4443
Polymers20,0011
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Germline-targeting HIV-1 gp120 engineered outer domain, eOD-GT6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4443
Polymers20,0011
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.960, 217.730, 44.990
Angle α, β, γ (deg.)90.00, 119.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Germline-targeting HIV-1 gp120 engineered outer domain, eOD-GT6


Mass: 20001.146 Da / Num. of mol.: 4
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
#2: 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.: 8
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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.38 Å3/Da / Density % sol: 48.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% w/v PEG3350, 0.2 M magnesium acetate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 22, 2012
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.489
11L, -K, H20.102
11H+L, -K, -L30.408
ReflectionResolution: 2.5→40 Å / Num. all: 25769 / Num. obs: 25751 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rsym value: 0.142 / Net I/σ(I): 8.1
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.43 / % possible all: 99.9

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Processing

Software
NameVersionClassification
JBluIce-EPICSdata collection
PHASERphasing
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TYG CHAIN A

3tyg


Resolution: 2.5→38.97 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.835 / SU B: 19.206 / SU ML: 0.217 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.139 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26159 1336 5.2 %RANDOM
Rwork0.20969 ---
obs0.21242 24371 99.71 %-
all-25769 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.897 Å2
Baniso -1Baniso -2Baniso -3
1--14.11 Å2-0 Å24.15 Å2
2--34.73 Å20 Å2
3----20.62 Å2
Refinement stepCycle: LAST / Resolution: 2.5→38.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5071 0 112 45 5228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0195299
X-RAY DIFFRACTIONr_bond_other_d0.0010.024816
X-RAY DIFFRACTIONr_angle_refined_deg1.1541.9657192
X-RAY DIFFRACTIONr_angle_other_deg0.7573.00611043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2785648
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20124.372247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.7315842
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7011536
X-RAY DIFFRACTIONr_chiral_restr0.070.2828
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215967
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021193
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 59 -
Rwork0.263 1696 -
obs--96.69 %
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)
10.42650.18250.13380.39250.01810.0823-0.00220.00180.0149-0.02030.0055-0.00210.0245-0.0088-0.00330.05920.00650.02190.0107-0.00490.096374.2264-7.188756.217
20.0713-0.11630.11350.42990.0340.3876-0.00470.0044-0.00610.0011-0.0002-0.0032-0.00510.01560.00490.0527-0.00670.02580.0160.00130.095956.764415.549372.4178
30.05690.0292-0.14380.31140.06520.4938-0.02740.0097-0.00610.00370.041-0.00830.0129-0.0164-0.01360.08010.0060.04280.00720.00180.098868.6465-38.126649.7512
40.3734-0.0328-0.33630.1918-0.06870.38090.0241-0.01980.0263-0.01320.0210.0018-0.03580.0116-0.04510.0986-0.00010.02340.0038-0.00430.087765.684546.809773.1774
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 170
2X-RAY DIFFRACTION1A201 - 202
3X-RAY DIFFRACTION2B1 - 172
4X-RAY DIFFRACTION2B201 - 202
5X-RAY DIFFRACTION3C1 - 174
6X-RAY DIFFRACTION3C201 - 202
7X-RAY DIFFRACTION4D1 - 174
8X-RAY DIFFRACTION4D201 - 202

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