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- PDB-4ka2: Crystal structure of CD4-mimetic miniprotein M48U12 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4ka2
TitleCrystal structure of CD4-mimetic miniprotein M48U12 in complex with HIV-1 YU2 gp120
Components
  • HIV-1 YU2 gp120
  • M48U12
KeywordsViral protein/INHIBITOR / VIRAL PROTEIN-PEPTIDE complex / HIV-1 / GP120 / YU2 / CD4 MIMIC / M48U12 / Viral protein-INHIBITOR complex
Function / homology
Function and homology information


Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Beta Complex / Mainly Beta
Similarity search - Domain/homology
CD4-MIMETIC MINIPROTEIN M48U12 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsAcharya, P. / Kwong, P.D.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Interfacial Cavity Filling To Optimize CD4-Mimetic Miniprotein Interactions with HIV-1 Surface Glycoprotein.
Authors: Morellato-Castillo, L. / Acharya, P. / Combes, O. / Michiels, J. / Descours, A. / Ramos, O.H. / Yang, Y. / Vanham, G. / Arien, K.K. / Kwong, P.D. / Martin, L. / Kessler, P.
History
DepositionApr 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 YU2 gp120
R: M48U12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,52110
Polymers44,7512
Non-polymers1,7708
Water4,252236
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.372, 163.441, 78.168
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-789-

HOH

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Components

#1: Protein HIV-1 YU2 gp120


Mass: 41695.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: YU2 / Gene: gp120 / Production host: Homo sapiens (human) / References: UniProt: P35961*PLUS
#2: Protein/peptide M48U12


Type: Peptide-like / Class: Inhibitor / Mass: 3055.819 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: DERIVED FROM SCYLLATOXIN (A SCORPION TOXIN) BY TRANSPLANTING THE GP120-INTERACTIVDERIVED FROM SCYLLATOXIN (A SCORPION TOXIN) BY TRANSPLANTING THE GP120-INTERACTIVE REGION OF CD4 ONTO THE ...Details: DERIVED FROM SCYLLATOXIN (A SCORPION TOXIN) BY TRANSPLANTING THE GP120-INTERACTIVDERIVED FROM SCYLLATOXIN (A SCORPION TOXIN) BY TRANSPLANTING THE GP120-INTERACTIVE REGION OF CD4 ONTO THE SCYLLATOXIN SCAFFOLD,E REGION OF CD4 ONTO THE SCYLLATOXIN SCAFFOLD,
References: CD4-MIMETIC MINIPROTEIN M48U12
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE CD4-MIMETIC MINIPROTEINS INHIBIT HIV-1 ENTRY AND ARE DERIVED FROM SCYLLATOXIN (A SCORPION TOXIN) ...THE CD4-MIMETIC MINIPROTEINS INHIBIT HIV-1 ENTRY AND ARE DERIVED FROM SCYLLATOXIN (A SCORPION TOXIN) BY TRANSPLANTING THE GP120-INTERACTIVE REGION OF CD4 ONTO THE SCYLLATOXIN SCAFFOLD, FOLLOWED BY MANY ROUNDS OF ITERATIVE OPTIMIZATION

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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: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 298 K / pH: 5.6
Details: 9.0% PEG 4000, 14.0% isopropanol, 100 mM sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 21, 2012
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.792→50 Å / Num. obs: 30289 / % possible obs: 92.3 % / Observed criterion σ(I): 1 / Redundancy: 5.5 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 12.4
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 1.3 / % possible all: 52

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→17.48 Å / SU ML: 0.21 / Isotropic thermal model: Isotropic / σ(F): 1.34 / Phase error: 26.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.228 1998 6.26 %
Rwork0.167 --
obs0.17 -81.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26 Å2
Refinement stepCycle: LAST / Resolution: 1.79→17.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2841 0 112 236 3189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133154
X-RAY DIFFRACTIONf_angle_d1.3724298
X-RAY DIFFRACTIONf_dihedral_angle_d14.3451176
X-RAY DIFFRACTIONf_chiral_restr0.082499
X-RAY DIFFRACTIONf_plane_restr0.007543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7919-1.83660.3218330.2804484X-RAY DIFFRACTION19
1.8366-1.88620.3614580.2668852X-RAY DIFFRACTION33
1.8862-1.94170.3187850.26381276X-RAY DIFFRACTION50
1.9417-2.00430.27431180.23771766X-RAY DIFFRACTION68
2.0043-2.07580.27211440.21042166X-RAY DIFFRACTION84
2.0758-2.15880.3061630.18782419X-RAY DIFFRACTION94
2.1588-2.25680.23351700.17972552X-RAY DIFFRACTION98
2.2568-2.37550.22191690.17132538X-RAY DIFFRACTION98
2.3755-2.5240.23561730.17772582X-RAY DIFFRACTION99
2.524-2.71820.25181720.18132596X-RAY DIFFRACTION100
2.7182-2.99050.261740.17782621X-RAY DIFFRACTION100
2.9905-3.42040.20691770.15952652X-RAY DIFFRACTION100
3.4204-4.29870.21041770.14152654X-RAY DIFFRACTION100
4.2987-17.48430.19041850.14542775X-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)
11.3322-0.2599-0.16931.21790.41991.3607-0.0404-0.00060.1452-0.03680.0441-0.0405-0.05340.0644-0.00380.2183-0.0035-0.02190.21520.00820.15818.5094-23.6641-0.8952
27.7928-1.19927.09120.5828-1.44377.2588-0.2671-0.71610.04720.47240.2749-0.50540.39991.5661-0.05070.50.2076-0.07650.8337-0.04680.340620.9574-31.507714.8943
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain R

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