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- PDB-4rqq: Crystal structure of human Fab PGDM1400, a broadly reactive and p... -

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Basic information

Entry
Database: PDB / ID: 4rqq
TitleCrystal structure of human Fab PGDM1400, a broadly reactive and potent HIV-1 neutralizing antibody
Components
  • Human anti-HIV-1 antibody PGDM1400 heavy chain
  • Human anti-HIV-1 antibody PGDM1400 light chain
KeywordsIMMUNE SYSTEM / IgG / anti-HIV-1 antibody / HIV-1 Env trimer
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsJulien, J.-P. / Wilson, I.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Recombinant HIV envelope trimer selects for quaternary-dependent antibodies targeting the trimer apex.
Authors: Sok, D. / van Gils, M.J. / Pauthner, M. / Julien, J.P. / Saye-Francisco, K.L. / Hsueh, J. / Briney, B. / Lee, J.H. / Le, K.M. / Lee, P.S. / Hua, Y. / Seaman, M.S. / Moore, J.P. / Ward, A.B. ...Authors: Sok, D. / van Gils, M.J. / Pauthner, M. / Julien, J.P. / Saye-Francisco, K.L. / Hsueh, J. / Briney, B. / Lee, J.H. / Le, K.M. / Lee, P.S. / Hua, Y. / Seaman, M.S. / Moore, J.P. / Ward, A.B. / Wilson, I.A. / Sanders, R.W. / Burton, D.R.
History
DepositionNov 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Database references
Revision 1.3Sep 20, 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 / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Human anti-HIV-1 antibody PGDM1400 light chain
H: Human anti-HIV-1 antibody PGDM1400 heavy chain
A: Human anti-HIV-1 antibody PGDM1400 light chain
B: Human anti-HIV-1 antibody PGDM1400 heavy chain
C: Human anti-HIV-1 antibody PGDM1400 light chain
D: Human anti-HIV-1 antibody PGDM1400 heavy chain


Theoretical massNumber of molelcules
Total (without water)151,6006
Polymers151,6006
Non-polymers00
Water00
1
L: Human anti-HIV-1 antibody PGDM1400 light chain
H: Human anti-HIV-1 antibody PGDM1400 heavy chain


Theoretical massNumber of molelcules
Total (without water)50,5332
Polymers50,5332
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-29 kcal/mol
Surface area21360 Å2
MethodPISA
2
A: Human anti-HIV-1 antibody PGDM1400 light chain
B: Human anti-HIV-1 antibody PGDM1400 heavy chain


Theoretical massNumber of molelcules
Total (without water)50,5332
Polymers50,5332
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-27 kcal/mol
Surface area21220 Å2
MethodPISA
3
C: Human anti-HIV-1 antibody PGDM1400 light chain
D: Human anti-HIV-1 antibody PGDM1400 heavy chain


Theoretical massNumber of molelcules
Total (without water)50,5332
Polymers50,5332
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-30 kcal/mol
Surface area21390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.700, 149.170, 109.930
Angle α, β, γ (deg.)90.00, 100.90, 90.00
Int Tables number4
Space group name H-MP1211
DetailsHeterodimer made of light chain and heavy chain

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Components

#1: Antibody Human anti-HIV-1 antibody PGDM1400 light chain


Mass: 24093.719 Da / Num. of mol.: 3 / Fragment: Fab light chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293F / Production host: HOMO SAPIENS (human)
#2: Antibody Human anti-HIV-1 antibody PGDM1400 heavy chain


Mass: 26439.633 Da / Num. of mol.: 3 / Fragment: Fab heavy chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293F / Production host: HOMO SAPIENS (human)
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: 2.96 Å3/Da / Density % sol: 58.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.04 M potassium dihydrogen phosphate, 16% w/v polyethylene glycol 8000 and 20% v/v glycerol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97947 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2014
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 3.1→40 Å / Num. all: 32022 / Num. obs: 30950 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 57.7 Å2 / Rmerge(I) obs: 0.167 / Net I/σ(I): 6.8
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 1.7 / Num. unique all: 2832 / % possible all: 98.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3U1S

3u1s


Resolution: 3.1→38.809 Å / SU ML: 0.43 / σ(F): 1.45 / Phase error: 25.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2528 1544 4.99 %RANDOM
Rwork0.2211 ---
obs0.2227 30926 96.7 %-
all-30926 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→38.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10427 0 0 0 10427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310687
X-RAY DIFFRACTIONf_angle_d0.76614525
X-RAY DIFFRACTIONf_dihedral_angle_d15.353829
X-RAY DIFFRACTIONf_chiral_restr0.0291633
X-RAY DIFFRACTIONf_plane_restr0.0041846
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.20.3331300.28872702X-RAY DIFFRACTION99
3.2-3.31440.32611540.27722704X-RAY DIFFRACTION98
3.3144-3.4470.32391320.27222698X-RAY DIFFRACTION98
3.447-3.60370.2861460.25072656X-RAY DIFFRACTION98
3.6037-3.79360.28011440.25312570X-RAY DIFFRACTION93
3.7936-4.0310.26471300.22522669X-RAY DIFFRACTION97
4.031-4.34190.23321420.19932715X-RAY DIFFRACTION98
4.3419-4.77810.18981440.18212662X-RAY DIFFRACTION96
4.7781-5.46790.22341330.18592632X-RAY DIFFRACTION95
5.4679-6.88270.23541480.22412727X-RAY DIFFRACTION98
6.8827-38.81240.24281410.19842647X-RAY DIFFRACTION94

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