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- PDB-4xcn: Crystal structure of human 4E10 Fab in complex with phosphatidic ... -

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Basic information

Entry
Database: PDB / ID: 4xcn
TitleCrystal structure of human 4E10 Fab in complex with phosphatidic acid (06:0 PA); 2.9 A resolution
Components
  • 4E10 Fab heavy chain
  • 4E10 Fab light chain
KeywordsIMMUNE SYSTEM / human anti gp41 HIV-1 4E10 Fab / membrane lipids / phosphatidic acid
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate / PHOSPHATE ION / Unknown ligand
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _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 1.4Oct 9, 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

Downloads & links

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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)286,57024
Polymers285,45712
Non-polymers1,11412
Water11,349630
1
L: 4E10 Fab light chain
H: 4E10 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9444
Polymers47,5762
Non-polymers3682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-18 kcal/mol
Surface area20120 Å2
MethodPISA
2
B: 4E10 Fab light chain
A: 4E10 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0375
Polymers47,5762
Non-polymers4603
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-17 kcal/mol
Surface area19830 Å2
MethodPISA
3
D: 4E10 Fab light chain
C: 4E10 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6714
Polymers47,5762
Non-polymers952
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-26 kcal/mol
Surface area19590 Å2
MethodPISA
4
F: 4E10 Fab light chain
E: 4E10 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6714
Polymers47,5762
Non-polymers952
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-31 kcal/mol
Surface area19190 Å2
MethodPISA
5
I: 4E10 Fab light chain
G: 4E10 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)47,5763
Polymers47,5762
Non-polymers01
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-18 kcal/mol
Surface area18950 Å2
MethodPISA
6
K: 4E10 Fab light chain
J: 4E10 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6714
Polymers47,5762
Non-polymers952
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-24 kcal/mol
Surface area19160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.890, 149.890, 469.760
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Antibody , 2 types, 12 molecules LBDFIKHACEGJ

#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)

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Non-polymers , 5 types, 642 molecules

#3: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 6 / Source method: obtained synthetically
#4: Chemical ChemComp-44E / (2R)-3-(phosphonooxy)propane-1,2-diyl dihexanoate


Mass: 368.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H29O8P / Comment: phospholipid*YM
#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
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 630 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsSIX UNKNOWN LIGANDS (UNL) HAVE BEEN MODELED. BASED ON ELECTRON DENSITY AND INTERACTION ...SIX 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-PHOSPHATE. 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: 2.72 Å3/Da / Density % sol: 54.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: Drop contains 10 mg/ml 4E10 Fab, 10 mM 06:0 PA mixed 1:1 v/v with a reservoir solution of 0.2 M potassium formate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2013
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: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.9→49.063 Å / Num. obs: 68834 / % possible obs: 98.1 % / Redundancy: 13.1 % / Biso Wilson estimate: 33.7 Å2 / Rsym value: 0.244 / Net I/σ(I): 12
Reflection shellResolution: 2.9→2.97 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.864 / Mean I/σ(I) obs: 3.2 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER2.5.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2FX7

2fx7


Resolution: 2.9→49.063 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2464 3442 5 %Random selection
Rwork0.1925 ---
obs0.1952 68834 98.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.3 Å2
Refinement stepCycle: LAST / Resolution: 2.9→49.063 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19435 0 166 630 20231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00320216
X-RAY DIFFRACTIONf_angle_d0.83627521
X-RAY DIFFRACTIONf_dihedral_angle_d12.1417162
X-RAY DIFFRACTIONf_chiral_restr0.0323137
X-RAY DIFFRACTIONf_plane_restr0.0053555
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.93890.32041350.25562547X-RAY DIFFRACTION96
2.9389-2.98090.28931340.252569X-RAY DIFFRACTION99
2.9809-3.02540.31641370.24982582X-RAY DIFFRACTION99
3.0254-3.07260.36891350.2562582X-RAY DIFFRACTION99
3.0726-3.1230.34231380.24312619X-RAY DIFFRACTION99
3.123-3.17680.25931350.23982563X-RAY DIFFRACTION99
3.1768-3.23460.28751360.2362586X-RAY DIFFRACTION99
3.2346-3.29680.31271360.22612578X-RAY DIFFRACTION99
3.2968-3.36410.29551370.22272603X-RAY DIFFRACTION99
3.3641-3.43720.2421360.20662597X-RAY DIFFRACTION99
3.4372-3.51710.25231360.20242586X-RAY DIFFRACTION99
3.5171-3.60510.27091390.19772617X-RAY DIFFRACTION99
3.6051-3.70250.30531350.22597X-RAY DIFFRACTION98
3.7025-3.81140.24051370.19392595X-RAY DIFFRACTION98
3.8114-3.93440.21761380.18532623X-RAY DIFFRACTION98
3.9344-4.07490.2281370.17792595X-RAY DIFFRACTION98
4.0749-4.2380.22261380.16992609X-RAY DIFFRACTION98
4.238-4.43080.20441370.15062619X-RAY DIFFRACTION98
4.4308-4.66420.21781380.14672619X-RAY DIFFRACTION98
4.6642-4.95620.18931380.15442606X-RAY DIFFRACTION97
4.9562-5.33840.21380.15982643X-RAY DIFFRACTION98
5.3384-5.87480.22151400.1682654X-RAY DIFFRACTION98
5.8748-6.72310.21781400.1782663X-RAY DIFFRACTION97
6.7231-8.46330.21631420.18682703X-RAY DIFFRACTION96
8.4633-49.070.20861500.18322837X-RAY DIFFRACTION95

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