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- PDB-2cmr: Crystal structure of the HIV-1 neutralizing antibody D5 Fab bound... -

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Basic information

Entry
Database: PDB / ID: 2cmr
TitleCrystal structure of the HIV-1 neutralizing antibody D5 Fab bound to the gp41 inner-core mimetic 5-helix
Components
  • (D5) x 2
  • TRANSMEMBRANE GLYCOPROTEIN
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN COMPLEX / NEUTRALIZATION / IMMUNOGLOBULIN / ENVELOPE PROTEIN / HIV / GP41 / AIDS / MHC I / MEMBRANE / TRANSMEMBRANE / IMMUNOGLOBULIN DOMAIN
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / membrane
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1860 / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Immunoglobulins / Up-down Bundle ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1860 / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Transmembrane glycoprotein / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS 1
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLuftig, M.A. / Mattu, M. / Di Giovine, P. / Geleziunas, R. / Hrin, R. / Barbato, G. / Bianchi, E. / Miller, M.D. / Pessi, A. / Carfi, A.
CitationJournal: 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
DepositionMay 11, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 8, 2017Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Dec 13, 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 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSMEMBRANE GLYCOPROTEIN
H: D5
L: D5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0174
Polymers70,9253
Non-polymers921
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)201.644, 41.618, 90.726
Angle α, β, γ (deg.)90.00, 110.55, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein TRANSMEMBRANE GLYCOPROTEIN / GP41


Mass: 25479.453 Da / Num. of mol.: 1 / Fragment: 5-HELIX, RESIDUES 543-582 AND 625-662
Source method: isolated from a genetically manipulated source
Details: SEQUENCE DERIVED FROM GENBANK 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 ...Details: SEQUENCE DERIVED FROM GENBANK 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 METHIONINE INITIATES AND A TAIL CONTAINS GGHHHHHHG
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 / Strain: HXB2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04578, UniProt: D0VWW0*PLUS
#2: Antibody D5 / FAB HEAVY CHAIN


Mass: 22756.447 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: IGG DERIVED FROM HUMAN B CELL LIBRARY / Plasmid: PEU3.2, PEU1.2 / Cell line (production host): 293-EBNA / Production host: Homo sapiens (human)
#3: Antibody D5 / FAB LIGHT CHAIN


Mass: 22689.236 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: IGG DERIVED FROM HUMAN B CELL LIBRARY / Plasmid: PEU3.2, PEU1.2 / Cell line (production host): 293-EBNA / Production host: Homo sapiens (human)
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growpH: 8.5
Details: 18% (W/V) PEG 4000, 0.2 M TRI-SODIUM CITRATE DIHYDRATE, 0.1 M TRIS-HCL / PH = 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 21, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→33.5 Å / Num. obs: 41190 / % possible obs: 90 % / Observed criterion σ(I): 3.5 / Redundancy: 2.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 8
Reflection shellResolution: 2→2.1 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.7 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AIK

1aik


Resolution: 2→33.52 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.907 / SU B: 4.936 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 2020 4.7 %RANDOM
Rwork0.209 ---
obs0.212 41190 93.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20.88 Å2
2--0.48 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 2→33.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4674 0 6 283 4963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0214775
X-RAY DIFFRACTIONr_bond_other_d0.0020.024234
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.9466483
X-RAY DIFFRACTIONr_angle_other_deg0.83239906
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5265596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.090.2742
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025287
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02889
X-RAY DIFFRACTIONr_nbd_refined0.1950.2906
X-RAY DIFFRACTIONr_nbd_other0.2380.24765
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0870.22910
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2233
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2320.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8271.53000
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5624826
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.42331775
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0194.51657
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→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.311 116
Rwork0.265 2679

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