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

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Basic information

Entry
Database: PDB / ID: 4jzw
TitleCrystal structure of CD4-mimetic miniprotein M48U1 in complex with HIV-1 YU2 gp120 in P212121 space group
Components
  • CD4-MIMETIC MINIPROTEIN M48U1
  • HIV-1 YU2 gp120 glycoprotein
KeywordsViral protein/INHIBITOR / glycoprotein / HIV-1 attachment glycoprotein / CD4-mimetic miniprotein / CD4 / 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 / 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 M48U1 / ISOPROPYL ALCOHOL / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.784 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 / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
G: HIV-1 YU2 gp120 glycoprotein
M: CD4-MIMETIC MINIPROTEIN M48U1
R: CD4-MIMETIC MINIPROTEIN M48U1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,22133
Polymers89,5044
Non-polymers4,71729
Water16,862936
1
A: HIV-1 YU2 gp120 glycoprotein
G: HIV-1 YU2 gp120 glycoprotein
M: CD4-MIMETIC MINIPROTEIN M48U1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,16432
Polymers86,4483
Non-polymers4,71729
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: HIV-1 YU2 gp120 glycoprotein
G: HIV-1 YU2 gp120 glycoprotein
R: CD4-MIMETIC MINIPROTEIN M48U1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,16432
Polymers86,4483
Non-polymers4,71729
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.651, 78.009, 163.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide / Sugars , 3 types, 22 molecules AGMR

#1: Protein HIV-1 YU2 gp120 glycoprotein


Mass: 41695.406 Da / Num. of mol.: 2
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 CD4-MIMETIC MINIPROTEIN M48U1


Type: Peptide-like / Class: Inhibitor / Mass: 3056.804 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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.: 18
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, 947 molecules

#4: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 936 / 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: 2.26 Å3/Da / Density % sol: 45.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.6
Details: 9% PEG 4000, 14% 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 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 11, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.784→50 Å / Num. all: 77460 / Num. obs: 64834 / % possible obs: 83.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 25.68 Å2 / Rsym value: 0.092 / Net I/σ(I): 22.9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.438 / % possible all: 74.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: dev_755)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.784→24.659 Å / SU ML: 0.18 / Isotropic thermal model: Isotropic / σ(F): 1.34 / Phase error: 25.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2088 3222 4.99 %
Rwork0.1637 --
obs0.166 64614 82.73 %
all-77460 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.7 Å2
Refinement stepCycle: LAST / Resolution: 1.784→24.659 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5720 0 298 936 6954
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096287
X-RAY DIFFRACTIONf_angle_d1.1068469
X-RAY DIFFRACTIONf_dihedral_angle_d13.382322
X-RAY DIFFRACTIONf_chiral_restr0.066990
X-RAY DIFFRACTIONf_plane_restr0.0051058
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7845-1.81110.3389900.27061582X-RAY DIFFRACTION49
1.8111-1.83940.32851340.25972520X-RAY DIFFRACTION80
1.8394-1.86950.23791440.22292682X-RAY DIFFRACTION84
1.8695-1.90170.26631560.20482686X-RAY DIFFRACTION85
1.9017-1.93630.2411420.19442760X-RAY DIFFRACTION86
1.9363-1.97350.25131510.1952706X-RAY DIFFRACTION85
1.9735-2.01380.24171330.18452769X-RAY DIFFRACTION86
2.0138-2.05760.22931330.17872786X-RAY DIFFRACTION86
2.0576-2.10540.21681330.17282763X-RAY DIFFRACTION87
2.1054-2.1580.21981280.16632754X-RAY DIFFRACTION86
2.158-2.21630.20411500.15932784X-RAY DIFFRACTION87
2.2163-2.28150.20071470.16022805X-RAY DIFFRACTION87
2.2815-2.35510.22111490.15842766X-RAY DIFFRACTION87
2.3551-2.43920.21311620.15532785X-RAY DIFFRACTION87
2.4392-2.53680.23631270.1612786X-RAY DIFFRACTION87
2.5368-2.65210.22871420.16362770X-RAY DIFFRACTION86
2.6521-2.79170.22031560.16682736X-RAY DIFFRACTION85
2.7917-2.96640.19261380.16872698X-RAY DIFFRACTION84
2.9664-3.1950.21241360.15642706X-RAY DIFFRACTION83
3.195-3.51570.2221400.15942683X-RAY DIFFRACTION82
3.5157-4.02250.19811480.1422645X-RAY DIFFRACTION81
4.0225-5.06070.17221380.13122634X-RAY DIFFRACTION80
5.0607-24.66090.17021450.17892586X-RAY DIFFRACTION75
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)
10.77780.0761-0.23870.7628-0.40621.2062-0.0252-0.13080.04490.1261-0.0053-0.0094-0.01560.05290.03120.26670.0122-0.01010.2482-0.01080.24958.431320.267317.4544
20.95880.14810.1441.28540.44130.9753-0.0124-0.139-0.00550.1343-0.00360.07670.0453-0.050.01410.23080.00840.0230.20640.01730.1856-8.4387-20.253917.5419
37.2988-3.6395-0.59364.9312.14011.9037-0.1038-0.0046-0.5601-0.3997-0.1948-0.79260.85370.61210.19070.46530.13410.13190.31190.09550.438220.62414.13798.8989
48.8783-6.53510.03456.5901-0.53823.6878-0.1939-0.20020.6015-0.02980.22150.9853-0.5436-0.2414-0.00560.36550.0487-0.06220.2252-0.01720.5052-21.4233-4.11749.8421
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain G
2X-RAY DIFFRACTION2chain A
3X-RAY DIFFRACTION3chain M
4X-RAY DIFFRACTION4chain R

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