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- PDB-4jzz: Crystal structure of CD4-mimetic miniprotein M48U1 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4jzz
TitleCrystal structure of CD4-mimetic miniprotein M48U1 in complex with HIV-1 YU2 gp120 in C2221 space group
Components
  • CD4-MIMETIC MINIPROTEIN M48U1
  • HIV-1 YU2 gp120 glycoprotein
KeywordsVIRAL PROTEIN/INHIBITOR / HIV-1 attachment protein gp120 / HIV-1 envelope / 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 / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / 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 M48U1 / CITRATE ANION / ISOPROPYL ALCOHOL / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsAcharya, P. / Kwong, P.D.
CitationJournal: Structure / Year: 2013
Title: Structural Basis for Highly Effective HIV-1 Neutralization by CD4-Mimetic Miniproteins Revealed by 1.5 A Cocrystal Structure of gp120 and M48U1.
Authors: Acharya, P. / Luongo, T.S. / Louder, M.K. / McKee, K. / Yang, Y. / Do Kwon, Y. / Mascola, J.R. / Kessler, P. / Martin, L. / Kwong, P.D.
History
DepositionApr 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.pdbx_role / _struct_conn.pdbx_value_order / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 YU2 gp120 glycoprotein
R: CD4-MIMETIC MINIPROTEIN M48U1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,14922
Polymers44,7522
Non-polymers2,39720
Water6,792377
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.087, 164.719, 78.031
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-874-

HOH

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Components

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Protein / Protein/peptide / Sugars , 3 types, 10 molecules AR

#1: Protein HIV-1 YU2 gp120 glycoprotein


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 / Plasmid: pVRC8400 / Production host: Homo sapiens (human) / References: UniProt: P35961*PLUS
#2: Protein/peptide CD4-MIMETIC MINIPROTEIN M48U1


Type: Peptide-like / Class: Inhibitor / Mass: 3056.804 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 M48U1
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / 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

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Non-polymers , 4 types, 389 molecules

#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 298 K / pH: 5.6
Details: 9.0% PEG 4000, 14.0% isopropanol, 100 mM sodium citrate, pH 5.6, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 19, 2010
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. obs: 68096 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Biso Wilson estimate: 21.55 Å2 / Rsym value: 0.117 / Net I/σ(I): 20.5
Reflection shellResolution: 1.49→1.52 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.585 / % possible all: 93

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→35.26 Å / SU ML: 0.14 / Isotropic thermal model: Isotropic / σ(F): 1.33 / Phase error: 19.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.189 3446 5.07 %
Rwork0.167 --
obs0.168 67985 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.55 Å2
Refinement stepCycle: LAST / Resolution: 1.49→35.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2843 0 151 377 3371
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063234
X-RAY DIFFRACTIONf_angle_d1.1914403
X-RAY DIFFRACTIONf_dihedral_angle_d13.2431247
X-RAY DIFFRACTIONf_chiral_restr0.064508
X-RAY DIFFRACTIONf_plane_restr0.005552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4912-1.51160.25241370.26932308X-RAY DIFFRACTION90
1.5116-1.53320.25551270.24662517X-RAY DIFFRACTION97
1.5332-1.55610.2391360.2352512X-RAY DIFFRACTION98
1.5561-1.58040.25981260.22252536X-RAY DIFFRACTION99
1.5804-1.60640.22261320.2042542X-RAY DIFFRACTION99
1.6064-1.6340.23141310.1972568X-RAY DIFFRACTION99
1.634-1.66380.23231490.19452589X-RAY DIFFRACTION100
1.6638-1.69580.20371420.19022542X-RAY DIFFRACTION99
1.6958-1.73040.19871340.19032564X-RAY DIFFRACTION100
1.7304-1.7680.21061390.18572584X-RAY DIFFRACTION100
1.768-1.80910.21131500.17222573X-RAY DIFFRACTION100
1.8091-1.85440.19861320.17272582X-RAY DIFFRACTION100
1.8544-1.90450.21281480.17582570X-RAY DIFFRACTION100
1.9045-1.96050.19761350.17442606X-RAY DIFFRACTION100
1.9605-2.02380.18011170.16342609X-RAY DIFFRACTION100
2.0238-2.09610.1941330.15762590X-RAY DIFFRACTION100
2.0961-2.180.17261400.162607X-RAY DIFFRACTION100
2.18-2.27930.18531380.15882603X-RAY DIFFRACTION100
2.2793-2.39940.15391410.15962608X-RAY DIFFRACTION100
2.3994-2.54970.20211260.16622621X-RAY DIFFRACTION100
2.5497-2.74650.20051510.16942618X-RAY DIFFRACTION100
2.7465-3.02270.18171280.1652641X-RAY DIFFRACTION100
3.0227-3.45980.1651310.16042661X-RAY DIFFRACTION100
3.4598-4.35770.1711630.14412653X-RAY DIFFRACTION100
4.3577-35.26910.2011600.16952735X-RAY DIFFRACTION99
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)
11.15960.07130.04471.27860.36691.3126-0.0736-0.0346-0.12680.03730.0449-0.010.06890.08670.02560.13370.01370.02380.12550.01690.0992-23.952623.70480.954
25.9126-0.6204-4.04871.6070.24252.7942-0.12210.69340.1011-0.79750.1159-0.4732-0.18061.01560.00750.4322-0.13320.1060.6146-0.01130.2444-11.038731.8623-14.6824
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain R

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