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- PDB-4nhc: Crystal structure of the HIV-1 neutralizing antibody 4E10 Fab fra... -

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Basic information

Entry
Database: PDB / ID: 4nhc
TitleCrystal structure of the HIV-1 neutralizing antibody 4E10 Fab fragment in complex with a hydrocarbon-stapled peptide containing the 4e10 epitope on gp41.
Components
  • FAB HEAVY CHAIN
  • FAB LIGHT CHAIN
  • MODIFIED FRAGMENT OF HIV GLYCOPROTEIN (GP41)
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN FOLD / BETA-SANDWICH / 4E10 FAB / ANTIBODY-EPITOPE COMPLEX / GP41 HIV-1 / HYDROCARBON STAPLE
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Stapled peptide (ACE)NWFNITN(DIV)LW(MK8)IKKKK / PHOSPHATE ION / trifluoroacetic acid
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.912 Å
AuthorsIrimia, A. / Wilson, I.A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Stapled HIV-1 peptides recapitulate antigenic structures and engage broadly neutralizing antibodies.
Authors: Bird, G.H. / Irimia, A. / Ofek, G. / Kwong, P.D. / Wilson, I.A. / Walensky, L.D.
History
DepositionNov 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Sep 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: FAB LIGHT CHAIN
H: FAB HEAVY CHAIN
P: MODIFIED FRAGMENT OF HIV GLYCOPROTEIN (GP41)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7986
Polymers49,4753
Non-polymers3233
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-43 kcal/mol
Surface area20070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)226.107, 226.107, 41.824
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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Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide MODIFIED FRAGMENT OF HIV GLYCOPROTEIN (GP41)


Type: Peptide-like / Class: Unknown / Mass: 2089.566 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: SYNTHETIC; THIS SEQUENCE INCLUDES A MODIFIED FRAGMENT OF THE HIV ENVELOPE PROTEIN GP41
References: Stapled peptide (ACE)NWFNITN(DIV)LW(MK8)IKKKK

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Antibody , 2 types, 2 molecules LH

#1: Antibody FAB LIGHT CHAIN


Mass: 23395.850 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO cells
#2: Antibody FAB HEAVY CHAIN


Mass: 23990.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO cells

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Non-polymers , 3 types, 32 molecules

#4: Chemical ChemComp-TFA / trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2HF3O2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE STAPLED PEPTIDES IN THE STRUCTURE WAS OBTAINED BY INCORPORATION OF (R)-2-(((9H-FLUOREN-9-YL) ...THE STAPLED PEPTIDES IN THE STRUCTURE WAS OBTAINED BY INCORPORATION OF (R)-2-(((9H-FLUOREN-9-YL)METHOXY)CARBONYLAMINO)-2-METHYL-PENT-4-ENOIC ACID AT THE POSITION 678 AND (S)-2-(((9H-FLUOREN-9-YL)METHOXY)CARBONYLAMINO)-2-METHYL-HEPT-6-ENOIC ACID AT THE POSITION 681

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: Reservoir solution: 0.2 M NaCl, 0.1 M Na/K Phosphate pH 6.2, 50% PEG 200, VAPOR DIFFUSION, SITTING DROP, temperature 22K, temperature 295K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 4, 2010
Details: K-B pair of biomorph mirrors for vertical and horizontal focusing
RadiationMonochromator: double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.91→48.95 Å / Num. all: 14400 / Num. obs: 13767 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 21.9 % / Biso Wilson estimate: 63.8 Å2 / Rmerge(I) obs: 0.182 / Net I/σ(I): 16.4
Reflection shellResolution: 2.91→2.96 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 3.1 / Num. unique all: 501 / % possible all: 70.4

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FX7

2fx7


Resolution: 2.912→48.95 Å / SU ML: 0.41 / σ(F): 1.34 / Phase error: 28.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2681 688 5.01 %RANDOM
Rwork0.2099 ---
obs0.2128 13737 95.47 %-
all-14389 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.064 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso mean: 69 Å2
Baniso -1Baniso -2Baniso -3
1--12.8238 Å20 Å20 Å2
2---12.8238 Å20 Å2
3---25.6475 Å2
Refinement stepCycle: LAST / Resolution: 2.912→48.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3485 0 19 29 3533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063710
X-RAY DIFFRACTIONf_angle_d0.7934905
X-RAY DIFFRACTIONf_dihedral_angle_d15.2691288
X-RAY DIFFRACTIONf_chiral_restr0.05546
X-RAY DIFFRACTIONf_plane_restr0.003628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.912-3.13680.39391120.31182121X-RAY DIFFRACTION80
3.1368-3.45240.30961370.24752617X-RAY DIFFRACTION97
3.4524-3.95180.28481410.20752677X-RAY DIFFRACTION100
3.9518-4.97810.22431440.16772730X-RAY DIFFRACTION100
4.9781-48.96050.25231540.21062904X-RAY DIFFRACTION100
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)
11.0952-0.3546-0.48660.92270.0580.2962-0.31440.0666-0.4310.05560.22690.37980.3578-0.0754-0.00020.5036-0.03020.10040.48510.09610.603166.6637-77.5302-0.61
20.71770.051-0.64830.4787-0.11050.5487-0.09110.07940.06810.11170.09480.173-0.0889-0.10440.00010.3976-0.035-0.01480.46340.11270.529540.7978-52.75255.1576
30.30090.2029-0.16151.2920.0340.8355-0.10360.10860.1405-0.1870.2677-0.1243-0.0834-0.02480.00010.3199-0.03880.05420.3860.02890.397978.0675-61.0961-9.5039
40.35240.5131-0.1810.8466-0.44540.34060.0804-0.17820.13460.1075-0.3398-0.2197-0.15550.082-00.4723-0.0847-0.0140.55070.08460.502253.5042-45.481410.3226
52.6733-1.79280.7811.47020.2122.26010.5057-0.3197-0.9156-0.8039-0.37520.20990.3412-0.566-0.0140.54460.03530.16110.36590.07580.62690.7667-77.3818-12.5171
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and ((resseq 1:108))
2X-RAY DIFFRACTION2chain 'L' and ((resseq 109:214))
3X-RAY DIFFRACTION3chain 'H' and ((resseq 1:113))
4X-RAY DIFFRACTION4chain 'H' and ((resseq 114:228))
5X-RAY DIFFRACTION5chain 'P' and ((resseq 670:686))

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