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- PDB-4xcy: Crystal structure of human 4E10 Fab in complex with phosphatidylg... -

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Basic information

Entry
Database: PDB / ID: 4xcy
TitleCrystal structure of human 4E10 Fab in complex with phosphatidylglycerol (06:0 PG)
Components
  • 4E10 Fab heavy chain
  • 4E10 Fab light chain
KeywordsIMMUNE SYSTEM / 4E10 Fab anti HIV-1 gp41 MPER / membrane lipids / phosphatidylglycerol
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-44G / Unknown ligand
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.96 Å
AuthorsIrimia, A. / Stanfield, R.L. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI084817 United States
CitationJournal: Immunity / Year: 2016
Title: Crystallographic Identification of Lipid as an Integral Component of the Epitope of HIV Broadly Neutralizing Antibody 4E10.
Authors: Irimia, A. / Sarkar, A. / Stanfield, R.L. / Wilson, I.A.
History
DepositionDec 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: 4E10 Fab light chain
H: 4E10 Fab heavy chain
B: 4E10 Fab light chain
A: 4E10 Fab heavy chain
D: 4E10 Fab light chain
C: 4E10 Fab heavy chain
F: 4E10 Fab light chain
E: 4E10 Fab heavy chain
I: 4E10 Fab light chain
G: 4E10 Fab heavy chain
K: 4E10 Fab light chain
J: 4E10 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)286,43420
Polymers285,45712
Non-polymers9778
Water00
1
L: 4E10 Fab light chain
H: 4E10 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0194
Polymers47,5762
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-18 kcal/mol
Surface area19970 Å2
MethodPISA
2
B: 4E10 Fab light chain
A: 4E10 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1115
Polymers47,5762
Non-polymers5353
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-19 kcal/mol
Surface area19620 Å2
MethodPISA
3
D: 4E10 Fab light chain
C: 4E10 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)47,5763
Polymers47,5762
Non-polymers01
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-18 kcal/mol
Surface area19370 Å2
MethodPISA
4
F: 4E10 Fab light chain
E: 4E10 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)47,5763
Polymers47,5762
Non-polymers01
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-18 kcal/mol
Surface area19450 Å2
MethodPISA
5
I: 4E10 Fab light chain
G: 4E10 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)47,5762
Polymers47,5762
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-24 kcal/mol
Surface area18890 Å2
MethodPISA
6
K: 4E10 Fab light chain
J: 4E10 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)47,5763
Polymers47,5762
Non-polymers01
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-17 kcal/mol
Surface area19220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.220, 150.220, 472.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Antibody
4E10 Fab light chain


Mass: 23395.850 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pDR12 / Cell line (production host): 293 Freestyle / Production host: Homo sapiens (human)
#2: Antibody
4E10 Fab heavy chain


Mass: 24180.250 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pDR12 / Cell line (production host): 293 Freestyle / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 5 / Source method: obtained synthetically
#4: Chemical ChemComp-44G / (2S)-3-{[(R)-{[(2R)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-2-(hexanoyloxy)propyl hexanoate


Mass: 442.438 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H35O10P
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
Has protein modificationY
Nonpolymer detailsFIVE UNKNOWN LIGANDS (UNL) HAVE BEEN MODELED. BASED ON ELECTRON DENSITY AND INTERACTION ...FIVE UNKNOWN LIGANDS (UNL) HAVE BEEN MODELED. BASED ON ELECTRON DENSITY AND INTERACTION ENVIRONMENTS, THE COMPOUNDS MAY BE FRAGMENTS OF POLYETHYLENE GLYCOL 3350 OR LIPID TAIL FRAGMENTS OF 1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHO-(1'-RAC-GLYCEROL). THE DATA ARE INSUFFICIENT TO DISTINGUISH BETWEEN THE TWO COMPOUNDS AND THE TRUE IDENTITY OF THE LIGAND IS UNKNOWN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: DROP CONTAINS 10 MG/ML 4E10 FAB, 10 MM PHOSPHATIDYLGLYCEROL (06:0 PG) MIXED 1:1 V/V WITH RESERVOIR SOLUTION OF 0.2 M SODIUM IODIDE, 20% PEG 3350, PH 6.0, VAPOR DIFFUSION, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2013
RadiationMonochromator: Liquid nitrogen-cooled double crystal, non fixed exit slit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.96→48.907 Å / Num. obs: 27268 / % possible obs: 95.5 % / Redundancy: 4.43 % / Biso Wilson estimate: 62.9 Å2 / Rsym value: 0.303 / Net I/σ(I): 5.2
Reflection shellResolution: 3.96→4.06 Å / Redundancy: 4.16 % / Rmerge(I) obs: 0.711 / Mean I/σ(I) obs: 2.1 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX1.7.2_869refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER2.5.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FX7

2fx7


Resolution: 3.96→48.907 Å / SU ML: 1.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.291 1362 5 %Random selection
Rwork0.244 ---
obs0.246 27257 95.6 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 24.77 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso mean: 77.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.4712 Å20 Å20 Å2
2--2.4712 Å20 Å2
3----4.9423 Å2
Refinement stepCycle: LAST / Resolution: 3.96→48.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19205 0 148 0 19353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00419893
X-RAY DIFFRACTIONf_angle_d0.98827102
X-RAY DIFFRACTIONf_dihedral_angle_d11.7056962
X-RAY DIFFRACTIONf_chiral_restr0.0493118
X-RAY DIFFRACTIONf_plane_restr0.0063499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.96-4.09760.29691340.28672551X-RAY DIFFRACTION98
4.0976-4.26160.32231370.25972604X-RAY DIFFRACTION99
4.2616-4.45540.27541380.23452600X-RAY DIFFRACTION98
4.4554-4.69020.30711370.22482608X-RAY DIFFRACTION98
4.6902-4.98370.30021320.2262532X-RAY DIFFRACTION95
4.9837-5.36810.24871330.24562516X-RAY DIFFRACTION94
5.3681-5.90750.28591380.23522618X-RAY DIFFRACTION98
5.9075-6.76040.32371380.27082626X-RAY DIFFRACTION96
6.7604-8.51010.33161330.2492521X-RAY DIFFRACTION91
8.5101-48.91030.2521420.23062719X-RAY DIFFRACTION91

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