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- PDB-4b50: Crystal structure of the HIV-1 gp41 MPER-specific llama VHH 2H10 -

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Basic information

Entry
Database: PDB / ID: 4b50
TitleCrystal structure of the HIV-1 gp41 MPER-specific llama VHH 2H10
Components2H10 LLAMA VHH
KeywordsIMMUNE SYSTEM / NEUTRALIZING ANTIBODY
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLAMA GLAMA (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsLutje Hulsik, D. / Sabin, C. / Macheboeuf, P. / Weissenhorn, W.
CitationJournal: Plos Pathog. / Year: 2013
Title: A Gp41 Mper-Specific Llama Vhh Requires a Hydrophobic Cdr3 for Neutralization But not for Antigen Recognition.
Authors: Lutje Hulsik, D. / Liu, Y.Y. / Strokappe, N.M. / Battella, S. / El Khattabi, M. / Mccoy, L.E. / Sabin, C. / Hinz, A. / Hock, M. / Macheboeuf, P. / Bonvin, A.M. / Langedijk, J.P. / Davis, D. ...Authors: Lutje Hulsik, D. / Liu, Y.Y. / Strokappe, N.M. / Battella, S. / El Khattabi, M. / Mccoy, L.E. / Sabin, C. / Hinz, A. / Hock, M. / Macheboeuf, P. / Bonvin, A.M. / Langedijk, J.P. / Davis, D. / Forsman Quigley, A. / Aasa-Chapman, M.M. / Seaman, M.S. / Ramos, A. / Poignard, P. / Favier, A. / Simorre, J.P. / Weiss, R.A. / Verrips, C.T. / Weissenhorn, W. / Rutten, L.
History
DepositionAug 2, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.2Nov 13, 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
A: 2H10 LLAMA VHH


Theoretical massNumber of molelcules
Total (without water)13,3521
Polymers13,3521
Non-polymers00
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.950, 89.950, 89.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-2032-

HOH

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Components

#1: Antibody 2H10 LLAMA VHH


Mass: 13351.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LAMA GLAMA (llama) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): GOLD
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
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: 2.21 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growpH: 9 / Details: 0.1 M BICINE, 3.2 M (NH4)2SO4, PH 9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 1.3→25 Å / Num. obs: 28043 / % possible obs: 99 % / Observed criterion σ(I): 2.2 / Redundancy: 13.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.1
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0116refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EZJ

3ezj


Resolution: 1.3→63.6 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.17963 1499 5.1 %RANDOM
Rwork0.14502 ---
obs0.1468 28043 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.105 Å2
Refinement stepCycle: LAST / Resolution: 1.3→63.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms935 0 0 172 1107
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191081
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.161.9571494
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9275152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.44423.09542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.32715182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1961510
X-RAY DIFFRACTIONr_chiral_restr0.0750.2165
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021854
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr29.36831081
X-RAY DIFFRACTIONr_sphericity_free05172
X-RAY DIFFRACTIONr_sphericity_bonded17.61151048
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.188 107 -
Rwork0.159 2091 -
obs--100 %

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