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- PDB-5ifa: Crystal structure of unbound VRC01c-HuGL2 Fab from an HIV-1 naive... -

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Basic information

Entry
Database: PDB / ID: 5ifa
TitleCrystal structure of unbound VRC01c-HuGL2 Fab from an HIV-1 naive donor at 1.82 A
Components(VRC01c-HuGL2 Fab ...) x 2
KeywordsIMMUNE SYSTEM / VRC01-class naive human germline antibody / CD4 binding site / anti-HIV-1
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.821 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 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: VRC01c-HuGL2 Fab heavy chain
L: VRC01c-HuGL2 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,31716
Polymers47,4312
Non-polymers1,88614
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-51 kcal/mol
Surface area19230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.063, 124.201, 47.946
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody VRC01c-HuGL2 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 VRC01c-HuGL2 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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Non-polymers , 4 types, 217 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.48 Å3/Da / Density % sol: 49.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M lithium sulfate and 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: Apr 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.82→48.84 Å / Num. obs: 40894 / % possible obs: 97.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 34.4 Å2 / CC1/2: 0.872 / Rsym value: 0.163 / Net I/σ(I): 0.95

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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: 1.821→48.837 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2403 2043 5 %
Rwork0.2048 --
obs0.2065 40836 94.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.821→48.837 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3253 0 79 203 3535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093445
X-RAY DIFFRACTIONf_angle_d1.0384673
X-RAY DIFFRACTIONf_dihedral_angle_d14.6292062
X-RAY DIFFRACTIONf_chiral_restr0.06511
X-RAY DIFFRACTIONf_plane_restr0.006588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8214-1.86370.3313730.30751369X-RAY DIFFRACTION51
1.8637-1.91030.38271340.28412560X-RAY DIFFRACTION95
1.9103-1.9620.30141380.25232618X-RAY DIFFRACTION97
1.962-2.01970.31221380.24592629X-RAY DIFFRACTION98
2.0197-2.08490.29981410.23952666X-RAY DIFFRACTION98
2.0849-2.15940.30011390.23672650X-RAY DIFFRACTION99
2.1594-2.24590.29951380.22162636X-RAY DIFFRACTION98
2.2459-2.34810.29771400.23492649X-RAY DIFFRACTION97
2.3481-2.47190.28841410.21782673X-RAY DIFFRACTION99
2.4719-2.62680.2431420.21492701X-RAY DIFFRACTION99
2.6268-2.82960.22661420.21692696X-RAY DIFFRACTION98
2.8296-3.11430.28621390.20072640X-RAY DIFFRACTION97
3.1143-3.56480.20361440.19162723X-RAY DIFFRACTION98
3.5648-4.49080.20441420.17472698X-RAY DIFFRACTION97
4.4908-48.85440.21391520.19952885X-RAY DIFFRACTION98
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)
11.5547-1.56830.78263.3795-1.26961.1155-0.0338-0.0017-0.1276-0.02080.0765-0.04640.0375-0.0779-0.04960.2448-0.01180.01540.3176-0.0190.353220.7268116.025816.0987
23.79131.7380.21887.75031.37952.19880.05290.02860.3463-0.44670.0102-0.4493-0.29270.1366-0.04440.3249-0.01330.04590.30140.02130.289114.12148.59166.4568
34.9508-0.87273.77772.126-0.1545.01560.22070.0662-0.3185-0.0771-0.1230.18890.0863-0.0291-0.12270.2565-0.01990.01450.2302-0.01460.33213.3795152.321216.696
41.7533-0.52080.57368.30280.68152.96240.0686-0.16-0.19220.4060.05240.00190.40680.0682-0.07760.26890.0007-0.00210.3220.00110.280824.5141129.686934.4776
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 1:118 )H1 - 118
2X-RAY DIFFRACTION2( CHAIN H AND RESID 119:214 )H119 - 214
3X-RAY DIFFRACTION3( CHAIN L AND RESID 111:212 )L111 - 212
4X-RAY DIFFRACTION4( CHAIN L AND RESID 1:110 )L1 - 110

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