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

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Basic information

Entry
Database: PDB / ID: 5ies
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 2.16 A
Components
  • (VRC01cHuGL2 Fab ...) x 2
  • Germline-targeting HIV-1 gp120 engineered outer domain eOD-GT8
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 / IMMUNE SYSTEM- VIRAL PROTEIN complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 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 1.3Nov 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
H: VRC01cHuGL2 Fab heavy chain
L: VRC01cHuGL2 Fab light chain
C: Germline-targeting HIV-1 gp120 engineered outer domain eOD-GT8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0398
Polymers67,3203
Non-polymers7195
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7090 Å2
ΔGint-17 kcal/mol
Surface area25830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.553, 138.604, 147.896
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody VRC01cHuGL2 Fab heavy chain


Mass: 23614.514 Da / Num. of mol.: 1
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 VRC01cHuGL2 Fab light chain


Mass: 23816.408 Da / Num. of mol.: 1
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, 3 molecules C

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


Mass: 19889.307 Da / Num. of mol.: 1
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)
#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.: 2 / 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, 190 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 4.06 Å3/Da / Density % sol: 69.73 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M citric acid (pH 4.0), 20% (w/v) PEG6000 with an overall pH 5.0 of the solution, 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: 2.1542→46.45 Å / Num. obs: 52709 / % possible obs: 92.5 % / Redundancy: 3.9 % / Biso Wilson estimate: 48.7 Å2 / CC1/2: 0.902 / Rsym value: 0.067 / Net I/σ(I): 16.2
Reflection shellResolution: 2.16→2.1933 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 1.9 / % possible all: 89.6

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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: 2.16→46.448 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2143 2606 4.96 %
Rwork0.1894 --
obs0.1906 52503 92.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.16→46.448 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4512 0 46 187 4745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064724
X-RAY DIFFRACTIONf_angle_d0.7826438
X-RAY DIFFRACTIONf_dihedral_angle_d13.9862865
X-RAY DIFFRACTIONf_chiral_restr0.051720
X-RAY DIFFRACTIONf_plane_restr0.004820
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.19930.25431380.25252539X-RAY DIFFRACTION91
2.1993-2.24160.25491450.24562712X-RAY DIFFRACTION96
2.2416-2.28730.29521300.23922679X-RAY DIFFRACTION96
2.2873-2.33710.24891410.22992712X-RAY DIFFRACTION96
2.3371-2.39140.27271380.23362680X-RAY DIFFRACTION96
2.3914-2.45120.26021540.22712657X-RAY DIFFRACTION95
2.4512-2.51750.26481320.22062708X-RAY DIFFRACTION95
2.5175-2.59160.29321450.22272650X-RAY DIFFRACTION95
2.5916-2.67520.25981370.21512658X-RAY DIFFRACTION94
2.6752-2.77080.24591310.21252594X-RAY DIFFRACTION91
2.7708-2.88180.25841240.21312499X-RAY DIFFRACTION89
2.8818-3.01290.25311460.19992675X-RAY DIFFRACTION94
3.0129-3.17170.2241410.20292662X-RAY DIFFRACTION94
3.1717-3.37040.23231480.19752624X-RAY DIFFRACTION93
3.3704-3.63050.22841330.19062624X-RAY DIFFRACTION92
3.6305-3.99570.20191310.17322574X-RAY DIFFRACTION90
3.9957-4.57340.15951310.15092505X-RAY DIFFRACTION87
4.5734-5.76030.14911320.15382600X-RAY DIFFRACTION89
5.7603-46.45880.22241290.19882545X-RAY DIFFRACTION84
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)
13.82380.0146-0.20383.77010.6973.6469-0.1669-0.5698-0.26290.19860.0891-0.34060.22640.26440.07690.42980.17480.05520.57860.03540.4646-10.3424-44.5681-27.6916
26.138-3.3251-1.66844.8541.91692.5837-0.08930.07310.1386-0.02950.1623-0.46760.00940.4841-0.06990.3765-0.00860.03240.3592-0.03820.291-34.7561-12.8459-19.8505
35.64012.8188-2.36974.8921-1.91094.0988-0.1307-0.2943-0.3380.1109-0.05940.11510.3982-0.06530.16390.38210.01720.05210.3089-0.01770.3285-65.3212-21.8409-4.0278
44.0052-0.3726-1.28360.23750.04771.1163-0.02020.1967-0.3453-0.1249-0.05090.11950.15390.10830.08670.46980.06070.05180.4549-0.11740.4751-37.1142-34.2883-29.521
53.5512-0.6925-0.14615.85820.7483.6762-0.081-0.03890.08-0.0704-0.03950.6251-0.271-0.36050.12520.3272-0.0485-0.03330.3235-0.06360.377-70.0535-22.8551-18.8558
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN C AND ( RESID 1:169 OR RESID 1001:1002 ) )C1 - 169
2X-RAY DIFFRACTION1( CHAIN C AND ( RESID 1:169 OR RESID 1001:1002 ) )C1001 - 1002
3X-RAY DIFFRACTION2( CHAIN L AND RESID 1:112 )L1 - 112
4X-RAY DIFFRACTION3( CHAIN L AND RESID 113:212 )L113 - 212
5X-RAY DIFFRACTION4( CHAIN H AND RESID 1:118 )H1 - 118
6X-RAY DIFFRACTION5( CHAIN H AND RESID 119:214 )H119 - 214

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