[English] 日本語
Yorodumi
- PDB-4orz: HIV-1 Nef protein in complex with single domain antibody sdAb19 a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4orz
TitleHIV-1 Nef protein in complex with single domain antibody sdAb19 and an engineered Hck SH3 domain
Components
  • Protein Nef
  • Tyrosine-protein kinase HCK
  • single domain antibody sdAb19
KeywordsTRANSFERASE/APOPTOSIS/IMMUNE SYSTEM / SH3 domain / immunglobolin fold / Antibodies / Epitopes / HIV Antibodies / HIV Accessory Proteins / PxxP motif / Complementarity Determining Regions / TRANSFERASE-APOPTOSIS-IMMUNE SYSTEM complex
Function / homology
Function and homology information


leukocyte degranulation / activation of transmembrane receptor protein tyrosine kinase activity / innate immune response-activating signaling pathway / leukocyte migration involved in immune response / respiratory burst after phagocytosis / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / regulation of podosome assembly / symbiont-mediated suppression of host autophagy / FLT3 signaling through SRC family kinases ...leukocyte degranulation / activation of transmembrane receptor protein tyrosine kinase activity / innate immune response-activating signaling pathway / leukocyte migration involved in immune response / respiratory burst after phagocytosis / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / regulation of podosome assembly / symbiont-mediated suppression of host autophagy / FLT3 signaling through SRC family kinases / regulation of phagocytosis / regulation of DNA-binding transcription factor activity / Nef and signal transduction / positive regulation of actin filament polymerization / Fc-gamma receptor signaling pathway involved in phagocytosis / mesoderm development / host cell Golgi membrane / FCGR activation / type II interferon-mediated signaling pathway / transport vesicle / Signaling by CSF3 (G-CSF) / phosphotyrosine residue binding / FCGR3A-mediated IL10 synthesis / cell surface receptor protein tyrosine kinase signaling pathway / lipopolysaccharide-mediated signaling pathway / peptidyl-tyrosine phosphorylation / integrin-mediated signaling pathway / cell projection / regulation of actin cytoskeleton organization / non-membrane spanning protein tyrosine kinase activity / FCGR3A-mediated phagocytosis / Regulation of signaling by CBL / non-specific protein-tyrosine kinase / negative regulation of inflammatory response to antigenic stimulus / Inactivation of CSF3 (G-CSF) signaling / caveola / SH3 domain binding / virion component / cytoplasmic side of plasma membrane / cytokine-mediated signaling pathway / Signaling by CSF1 (M-CSF) in myeloid cells / regulation of cell shape / protein autophosphorylation / regulation of inflammatory response / protein tyrosine kinase activity / cell differentiation / cytoskeleton / lysosome / protein phosphorylation / cell adhesion / defense response to Gram-positive bacterium / intracellular signal transduction / endocytosis involved in viral entry into host cell / inflammatory response / signaling receptor binding / focal adhesion / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / lipid binding / negative regulation of apoptotic process / GTP binding / host cell plasma membrane / Golgi apparatus / extracellular region / ATP binding / nucleus / membrane / plasma membrane / cytosol
Similarity search - Function
Nef Regulatory Factor / Nef Regulatory Factor / Tyrosine-protein kinase HCK, SH2 domain / HIV-1 Nef protein, anchor domain superfamily / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / SH3 Domains / : / SH3 domain ...Nef Regulatory Factor / Nef Regulatory Factor / Tyrosine-protein kinase HCK, SH2 domain / HIV-1 Nef protein, anchor domain superfamily / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Protein Nef / Tyrosine-protein kinase HCK
Similarity search - Component
Biological speciesHomo sapiens (human)
HIV-1 M:B_ARV2/SF2 (virus)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGeyer, M. / Lulf, S.
CitationJournal: Retrovirology / Year: 2014
Title: Structural basis for the inhibition of HIV-1 Nef by a high-affinity binding single-domain antibody.
Authors: Lulf, S. / Matz, J. / Rouyez, M.C. / Jarviluoma, A. / Saksela, K. / Benichou, S. / Geyer, M.
History
DepositionFeb 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tyrosine-protein kinase HCK
B: Protein Nef
C: single domain antibody sdAb19


Theoretical massNumber of molelcules
Total (without water)37,4403
Polymers37,4403
Non-polymers00
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.000, 73.000, 71.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein Tyrosine-protein kinase HCK / Hematopoietic cell kinase / Hemopoietic cell kinase / p59-HCK/p60-HCK / p59Hck / p61Hck


Mass: 7614.431 Da / Num. of mol.: 1 / Fragment: SH3 domain, UNP residues 77-138 / Mutation: E90Y, A91S, I92P, H93F, H94S, E95W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HCK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P08631, non-specific protein-tyrosine kinase
#2: Protein Protein Nef / 3'ORF / Negative factor / F-protein / C-terminal core protein


Mass: 16817.979 Da / Num. of mol.: 1 / Fragment: Nef protein, UNP residues 45-210 / Mutation: I47M, T48A, C59S, C210A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 M:B_ARV2/SF2 (virus) / Gene: nef / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03407
#3: Antibody single domain antibody sdAb19


Mass: 13007.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: About 0.1 micro L of protein solution at 10 mg/ml concentration was mixed with 0.1 micro L of reservoir solution from a 70 L reservoir in 96-well Hampton 3553 crystallization plates. Initial ...Details: About 0.1 micro L of protein solution at 10 mg/ml concentration was mixed with 0.1 micro L of reservoir solution from a 70 L reservoir in 96-well Hampton 3553 crystallization plates. Initial crystals of NefSF2 sdAb19 SH3B6 could be obtained in 0.2 M potassium formate and 20% polyethylene glycol (PEG) 3350. Crystal conditions were optimized to 0.2 M potassium formate, 17.5% polyethylene glycol (PEG) 3350 and 0.35 M ammonium chloride grown by hanging-drop vapor diffusion in Linbro crystallization plates. , pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9794 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2012
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→41.75 Å / Num. obs: 47918 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 2.1→2.15 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RBB

3rbb


Resolution: 2→41.75 Å / SU ML: 0.21 / σ(F): 2.04 / Phase error: 24.91 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2364 1252 5 %random
Rwork0.2018 ---
obs0.2036 25031 98.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→41.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2330 0 0 125 2455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082399
X-RAY DIFFRACTIONf_angle_d1.2883255
X-RAY DIFFRACTIONf_dihedral_angle_d15.518865
X-RAY DIFFRACTIONf_chiral_restr0.085336
X-RAY DIFFRACTIONf_plane_restr0.006413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.08010.29151380.252628X-RAY DIFFRACTION98
2.0801-2.17480.27121370.23972592X-RAY DIFFRACTION99
2.1748-2.28940.27151380.23422624X-RAY DIFFRACTION98
2.2894-2.43280.29921390.23872638X-RAY DIFFRACTION99
2.4328-2.62060.26511390.23492645X-RAY DIFFRACTION99
2.6206-2.88430.24121380.21892621X-RAY DIFFRACTION99
2.8843-3.30150.23911400.21622658X-RAY DIFFRACTION99
3.3015-4.1590.21941390.17842656X-RAY DIFFRACTION99
4.159-41.760.2011440.16862717X-RAY DIFFRACTION100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more