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- PDB-2xra: crystal structure of the HK20 Fab in complex with a gp41 mimetic ... -

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Basic information

Entry
Database: PDB / ID: 2xra
Titlecrystal structure of the HK20 Fab in complex with a gp41 mimetic 5- Helix
Components
  • HK20, HUMAN MONOCLONAL ANTIBODY HEAVY CHAIN
  • HK20, HUMAN MONOCLONAL ANTIBODY LIGHT CHAIN
  • TRANSMEMBRANE PROTEIN GP41
KeywordsIMMUNE SYSTEM / ANTIBODY / MONOCLONAL CELLS / NEUTRALIZATION TESTS
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / actin filament organization / host cell endosome membrane ...Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / actin filament organization / host cell endosome membrane / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / receptor ligand activity / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesSYNTHETIC CONSTRUCT (others)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSabin, C. / Corti, D. / Buzon, V. / Seaman, M.S. / Lutje Hulsik, D. / Hinz, A. / Vanzetta, F. / Agatic, G. / Silacci, C. / Langedijk, J.P.M. ...Sabin, C. / Corti, D. / Buzon, V. / Seaman, M.S. / Lutje Hulsik, D. / Hinz, A. / Vanzetta, F. / Agatic, G. / Silacci, C. / Langedijk, J.P.M. / Mainetti, L. / Scarlatti, G. / Sallusto, F. / Weiss, R. / Lanzavecchia, A. / Weissenhorn, W.
Citation
Journal: PLoS Pathog. / Year: 2010
Title: Crystal structure and size-dependent neutralization properties of HK20, a human monoclonal antibody binding to the highly conserved heptad repeat 1 of gp41.
Authors: Sabin, C. / Corti, D. / Buzon, V. / Seaman, M.S. / Lutje Hulsik, D. / Hinz, A. / Vanzetta, F. / Agatic, G. / Silacci, C. / Mainetti, L. / Scarlatti, G. / Sallusto, F. / Weiss, R. / ...Authors: Sabin, C. / Corti, D. / Buzon, V. / Seaman, M.S. / Lutje Hulsik, D. / Hinz, A. / Vanzetta, F. / Agatic, G. / Silacci, C. / Mainetti, L. / Scarlatti, G. / Sallusto, F. / Weiss, R. / Lanzavecchia, A. / Weissenhorn, W.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Structural Basis for HIV-1 Neutralization by a Gp41 Fusion Intermediate-Directed Antibody.
Authors: Luftig, M.A. / Mattu, M. / Di Giovine, P. / Geleziunas, R. / Hrin, R. / Barbato, G. / Bianchi, E. / Miller, M.D. / Pessi, A. / Carfi, A.
History
DepositionSep 13, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references / Version format compliance
Revision 1.2Feb 7, 2018Group: Database references / Source and taxonomy / Structure summary
Category: audit_author / citation / entity_src_gen
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Dec 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 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSMEMBRANE PROTEIN GP41
H: HK20, HUMAN MONOCLONAL ANTIBODY HEAVY CHAIN
L: HK20, HUMAN MONOCLONAL ANTIBODY LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)72,9613
Polymers72,9613
Non-polymers00
Water2,126118
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-35 kcal/mol
Surface area29150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.947, 62.710, 76.610
Angle α, β, γ (deg.)90.00, 97.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TRANSMEMBRANE PROTEIN GP41


Mass: 25721.725 Da / Num. of mol.: 1
Fragment: 5-HELIX INNER-CORE MIMETIC COMPRISED OF REPEATS OF RESIDUES 543-582 AND 625-662
Source method: isolated from a genetically manipulated source
Details: SEQUENCE DERIVED FROM UNIPROT AC P04578 WHERE THREE REGIONS EACH EQUIVALENT TO AA 543-582 ARE INTERSPERSED BY TWO DIFFERENT REGIONS (EACH EQUIVALENT TO AA 625-662). LINKERS GGSGG AND GSSGG ...Details: SEQUENCE DERIVED FROM UNIPROT AC P04578 WHERE THREE REGIONS EACH EQUIVALENT TO AA 543-582 ARE INTERSPERSED BY TWO DIFFERENT REGIONS (EACH EQUIVALENT TO AA 625-662). LINKERS GGSGG AND GSSGG JOIN THE REGIONS AND ALTERNATE STARTING WITH GGSGG. A
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Production host: ESCHERICHIA COLI BL21(DE3) / Variant (production host): Gold / References: UniProt: P04578
#2: Antibody HK20, HUMAN MONOCLONAL ANTIBODY HEAVY CHAIN


Mass: 23609.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell: MEMORY B-LYMPHOCYTE / Tissue: BLOOD
#3: Antibody HK20, HUMAN MONOCLONAL ANTIBODY LIGHT CHAIN


Mass: 23630.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell: MEMORY B-LYMPHOCYTE / Tissue: BLOOD
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.56 Å3/Da / Density % sol: 52.05 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1 M HEPES PH 7.5, 0.2 M AMMONIUM SULPHATE, 25% PEG 3350 (W/V)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.9765
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.3→37 Å / Num. obs: 28254 / % possible obs: 93.3 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 4
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.1 / % possible all: 89.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CMR

2cmr


Resolution: 2.3→37.63 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.887 / SU B: 8.729 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.454 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED LOOPS REGIONS OF GP41-5HB WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.27943 1509 5.1 %RANDOM
Rwork0.23693 ---
obs0.23913 28253 93.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.977 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å2-0.2 Å2
2--0.06 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 2.3→37.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4962 0 0 118 5080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225057
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1831.9496862
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.425634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.44325.426223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.17515872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2431521
X-RAY DIFFRACTIONr_chiral_restr0.0740.2781
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213780
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_it0.6221.53179
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1925131
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.64931878
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8984.51731
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 96 -
Rwork0.284 1961 -
obs--89.05 %

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