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- PDB-3o2d: Crystal structure of HIV-1 primary receptor CD4 in complex with a... -

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Basic information

Entry
Database: PDB / ID: 3o2d
TitleCrystal structure of HIV-1 primary receptor CD4 in complex with a potent antiviral antibody
Components
  • T-cell surface glycoprotein CD4
  • ibalizumab heavy chain
  • ibalizumab light chain
KeywordsIMMUNE SYSTEM / immunoglobulin fold / HIV-1 primary receptor / T cell coreceptor / monoclonal antibody / Membrane
Function / homology
Function and homology information


helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / T cell selection / MHC class II protein binding / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / positive regulation of monocyte differentiation / Nef Mediated CD4 Down-regulation ...helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / T cell selection / MHC class II protein binding / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / positive regulation of monocyte differentiation / Nef Mediated CD4 Down-regulation / Alpha-defensins / positive regulation of kinase activity / regulation of T cell activation / extracellular matrix structural constituent / T cell receptor complex / Other interleukin signaling / enzyme-linked receptor protein signaling pathway / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / regulation of calcium ion transport / macrophage differentiation / Generation of second messenger molecules / T cell differentiation / PD-1 signaling / positive regulation of protein kinase activity / Binding and entry of HIV virion / coreceptor activity / cell surface receptor protein tyrosine kinase signaling pathway / T cell activation / positive regulation of calcium-mediated signaling / positive regulation of interleukin-2 production / protein tyrosine kinase binding / Vpu mediated degradation of CD4 / calcium-mediated signaling / clathrin-coated endocytic vesicle membrane / transmembrane signaling receptor activity / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of T cell activation / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / MHC class II protein complex binding / Clathrin-mediated endocytosis / virus receptor activity / signaling receptor activity / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-negative bacterium / adaptive immune response / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / positive regulation of viral entry into host cell / early endosome / cell surface receptor signaling pathway / cell adhesion / immune response / positive regulation of protein phosphorylation / membrane raft / endoplasmic reticulum lumen / external side of plasma membrane / lipid binding / endoplasmic reticulum membrane / protein kinase binding / positive regulation of DNA-templated transcription / enzyme binding / signal transduction / protein homodimerization activity / zinc ion binding / identical protein binding / plasma membrane
Similarity search - Function
CD4, extracellular / T cell CD4 receptor C-terminal region / CD4, extracellular / T cell CD4 receptor C terminal region / T-cell surface antigen CD4 / Immunoglobulin C2-set / Immunoglobulin C2-set domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype 2 ...CD4, extracellular / T cell CD4 receptor C-terminal region / CD4, extracellular / T cell CD4 receptor C terminal region / T-cell surface antigen CD4 / Immunoglobulin C2-set / Immunoglobulin C2-set domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
T-cell surface glycoprotein CD4
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsFreeman, M.M. / Seaman, M.S. / Rits-Volloch, S. / Hong, X. / Ho, D.D. / Chen, B.
CitationJournal: Structure / Year: 2010
Title: Crystal Structure of HIV-1 Primary Receptor CD4 in Complex with a Potent Antiviral Antibody.
Authors: Freeman, M.M. / Seaman, M.S. / Rits-Volloch, S. / Hong, X. / Kao, C.Y. / Ho, D.D. / Chen, B.
History
DepositionJul 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: ibalizumab light chain
H: ibalizumab heavy chain
A: T-cell surface glycoprotein CD4


Theoretical massNumber of molelcules
Total (without water)69,5783
Polymers69,5783
Non-polymers00
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-30 kcal/mol
Surface area27450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.164, 66.266, 266.659
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody ibalizumab light chain


Mass: 24245.900 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): NS/O / Production host: Mus musculus (house mouse)
#2: Antibody ibalizumab heavy chain


Mass: 24302.010 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): NS/O / Production host: Mus musculus (house mouse)
#3: Protein T-cell surface glycoprotein CD4 / T-cell surface antigen T4/Leu-3


Mass: 21029.857 Da / Num. of mol.: 1 / Fragment: UNP residues 26-207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD4 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P01730
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

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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: 3.31 Å3/Da / Density % sol: 62.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 3 M Na malonate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 4, 2009
RadiationMonochromator: Cryo-Cooled Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.19→48.6 Å / Num. all: 48479 / Num. obs: 45445 / % possible obs: 93.5 %
Reflection shellResolution: 2.19→2.25 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 2836 / Rsym value: 0.631 / % possible all: 89.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→48.6 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 11.181 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2242 2295 5.1 %RANDOM
Rwork0.19206 ---
obs0.19369 43149 93.74 %-
all-45445 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.913 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å2-0 Å2
2--0.96 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 2.19→48.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4751 0 0 215 4966
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224858
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.9576599
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6215613
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.31125.101198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.17415831
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3261517
X-RAY DIFFRACTIONr_chiral_restr0.1050.2747
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213623
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_it0.8971.53065
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7324970
X-RAY DIFFRACTIONr_scbond_it2.58231793
X-RAY DIFFRACTIONr_scangle_it4.2684.51629
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.19→2.252 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 152 -
Rwork0.259 2836 -
obs--85.35 %
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)
11.7315-0.01861.35270.24760.03581.71380.0243-0.09490.07090.1214-0.07260.00810.0215-0.17030.04830.1293-0.0236-0.00060.26840.00820.08723.75815.59257.388
22.116-0.58131.37050.3255-0.66981.53940.21060.4124-0.16050.0191-0.14950.01150.11090.298-0.0610.15530.0304-0.03050.3242-0.01740.097413.2515.86246.16
32.6421.2648-0.74431.17620.14882.7514-0.04560.6024-0.0487-0.14480.07670.10120.1514-0.0872-0.03110.07590.0514-0.0470.731-0.03520.043-12.8969.34712.078
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L-10 - 9999
2X-RAY DIFFRACTION2H-10 - 9999
3X-RAY DIFFRACTION3A-10 - 9999

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