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- PDB-5if0: Crystal structure of VRC01c-HuGL2 Fab from an HIV-1 naive donor i... -

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Basic information

Entry
Database: PDB / ID: 5if0
TitleCrystal structure of VRC01c-HuGL2 Fab from an HIV-1 naive donor in complex with with a germline-targeting gp120 engineered outer domain eOD-GT8 at 2.44 A
Components
  • Germline-targeting HIV-1 gp120 engineered outer domain eOD-GT8
  • VRC01c-HuGL2 Fab light chain
  • VRC01cHuGL2 Fab heavy chain
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / HIV-1 gp120 / engineered outer domain (eOD) / germline targeting / CD4 binding site / VRC01-class naive human germline antibody / immune system / viral-protein complex / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsSarkar, A. / Wilson, I.A.
CitationJournal: Science / Year: 2016
Title: HIV-1 broadly neutralizing antibody precursor B cells revealed by germline-targeting immunogen.
Authors: Jardine, J.G. / Kulp, D.W. / Havenar-Daughton, C. / Sarkar, A. / Briney, B. / Sok, D. / Sesterhenn, F. / Ereno-Orbea, J. / Kalyuzhniy, O. / Deresa, I. / Hu, X. / Spencer, S. / Jones, M. / ...Authors: Jardine, J.G. / Kulp, D.W. / Havenar-Daughton, C. / Sarkar, A. / Briney, B. / Sok, D. / Sesterhenn, F. / Ereno-Orbea, J. / Kalyuzhniy, O. / Deresa, I. / Hu, X. / Spencer, S. / Jones, M. / Georgeson, E. / Adachi, Y. / Kubitz, M. / deCamp, A.C. / Julien, J.P. / Wilson, I.A. / Burton, D.R. / Crotty, S. / Schief, W.R.
History
DepositionFeb 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / 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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Sep 27, 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
Revision 1.3Oct 16, 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
A: VRC01cHuGL2 Fab heavy chain
B: VRC01c-HuGL2 Fab light chain
G: Germline-targeting HIV-1 gp120 engineered outer domain eOD-GT8
H: VRC01cHuGL2 Fab heavy chain
I: Germline-targeting HIV-1 gp120 engineered outer domain eOD-GT8
L: VRC01c-HuGL2 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,62011
Polymers134,6406
Non-polymers9805
Water1,36976
1
A: VRC01cHuGL2 Fab heavy chain
B: VRC01c-HuGL2 Fab light chain
I: Germline-targeting HIV-1 gp120 engineered outer domain eOD-GT8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7635
Polymers67,3203
Non-polymers4422
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
G: Germline-targeting HIV-1 gp120 engineered outer domain eOD-GT8
H: VRC01cHuGL2 Fab heavy chain
L: VRC01c-HuGL2 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8586
Polymers67,3203
Non-polymers5373
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)174.192, 147.578, 103.685
Angle α, β, γ (deg.)90.00, 126.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Antibody , 2 types, 4 molecules AHBL

#1: Antibody VRC01cHuGL2 Fab heavy chain


Mass: 23614.514 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pFUSEss-CHIg-hG1 / Cell line (production host): HEK 293 Freestyle / Production host: Homo sapiens (human)
#2: Antibody VRC01c-HuGL2 Fab light chain


Mass: 23816.408 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pFUSEss-CHIg-hG1 / Cell line (production host): HEK 293 Freestyle / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 6 molecules GI

#3: Protein Germline-targeting HIV-1 gp120 engineered outer domain eOD-GT8


Mass: 19889.307 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHLsec / Cell line (production host): HEK 293S / Production host: Homo sapiens (human)
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / 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, 77 molecules

#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.97 Å3/Da / Density % sol: 69.04 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M potassium dihydrogen phosphate, 20% (w/v) PEG3350 and cryo-protected with 25% glycerol

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.408→44.444 Å / Num. obs: 73979 / % possible obs: 95.2 % / Redundancy: 2.8 % / Biso Wilson estimate: 47.6 Å2 / CC1/2: 0.849 / Rsym value: 0.0102 / Net I/σ(I): 9.2
Reflection shellResolution: 2.4082→2.4399 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.778 / Mean I/σ(I) obs: 1.1 / % possible all: 94.2

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
HKL-2000v706edata reduction
HKL-2000v706edata scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JPK

4jpk


Resolution: 2.44→44.444 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2319 3676 5.01 %
Rwork0.1908 --
obs0.1929 73411 94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.44→44.444 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8944 0 61 76 9081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059324
X-RAY DIFFRACTIONf_angle_d0.74512719
X-RAY DIFFRACTIONf_dihedral_angle_d13.9645615
X-RAY DIFFRACTIONf_chiral_restr0.0491435
X-RAY DIFFRACTIONf_plane_restr0.0051618
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.47210.3781940.33851898X-RAY DIFFRACTION66
2.4721-2.5060.36851410.30842653X-RAY DIFFRACTION94
2.506-2.54180.35241510.29032725X-RAY DIFFRACTION95
2.5418-2.57970.321390.27852686X-RAY DIFFRACTION96
2.5797-2.620.31931390.27672692X-RAY DIFFRACTION96
2.62-2.6630.29841600.26682707X-RAY DIFFRACTION95
2.663-2.70890.31271300.25332714X-RAY DIFFRACTION95
2.7089-2.75810.32841310.26922611X-RAY DIFFRACTION93
2.7581-2.81120.33631210.25472508X-RAY DIFFRACTION87
2.8112-2.86850.32921410.26482616X-RAY DIFFRACTION92
2.8685-2.93090.25271400.25432775X-RAY DIFFRACTION98
2.9309-2.99910.26121520.22282820X-RAY DIFFRACTION98
2.9991-3.07410.24591490.22282736X-RAY DIFFRACTION98
3.0741-3.15710.21091460.20422798X-RAY DIFFRACTION98
3.1571-3.250.23841290.21172788X-RAY DIFFRACTION97
3.25-3.35490.26631590.21062735X-RAY DIFFRACTION96
3.3549-3.47470.2841480.20452736X-RAY DIFFRACTION96
3.4747-3.61380.27221290.19542627X-RAY DIFFRACTION93
3.6138-3.77820.26291340.1852574X-RAY DIFFRACTION89
3.7782-3.97730.18561550.16122763X-RAY DIFFRACTION98
3.9773-4.22630.22231350.14692805X-RAY DIFFRACTION97
4.2263-4.55230.15991520.13442771X-RAY DIFFRACTION97
4.5523-5.00990.17591500.13182740X-RAY DIFFRACTION97
5.0099-5.73350.15161420.14892661X-RAY DIFFRACTION93
5.7335-7.21860.23951590.18432823X-RAY DIFFRACTION99
7.2186-44.45330.19231500.17582773X-RAY DIFFRACTION95
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)
12.37470.19510.10692.95180.0863.44790.1755-0.13450.37860.10710.01350.3666-0.1428-0.4358-0.18650.2816-0.04310.08350.4145-0.00940.5656169.957413.750547.9909
23.3081-0.3467-0.23942.71210.06673.0153-0.0740.4211-0.1176-0.3257-0.0189-0.01290.54910.06270.09930.57940.0130.01090.40040.04620.248219.066268.2809-18.0027
32.02720.5087-0.96511.7832-0.9732.52380.00910.0837-0.0596-0.1384-0.0320.05290.0583-0.07490.0660.30780.0361-0.04710.2213-0.00580.3062217.623853.179129.7273
41.04860.4135-1.31721.2391-0.91313.2978-0.05290.09150.1255-0.06240.06260.0429-0.0963-0.25020.00550.32760.0826-0.05140.34120.05080.3485206.83466.129823.5578
52.44490.8284-1.95651.2096-0.89772.01830.02030.2705-0.1829-0.01690.04080.04680.0868-0.1282-0.08450.301-0.0731-0.04230.3624-0.0940.3562206.681616.345924.0251
61.70410.6132-0.72991.6939-0.58832.31550.01830.02790.00390.0028-0.03040.1545-0.0194-0.08620.00580.2829-0.0066-0.03970.2274-0.0290.3459215.286228.828732.9302
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'G'
2X-RAY DIFFRACTION2chain 'I'
3X-RAY DIFFRACTION3chain 'B'
4X-RAY DIFFRACTION4chain 'A'
5X-RAY DIFFRACTION5chain 'H'
6X-RAY DIFFRACTION6chain 'L'

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