[English] 日本語
Yorodumi
- PDB-2v4h: NEMO CC2-LZ domain - 1D5 DARPin complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2v4h
TitleNEMO CC2-LZ domain - 1D5 DARPin complex
Components
  • 1D5 DARPIN
  • NF-KAPPA-B ESSENTIAL MODULATOR
KeywordsTRANSCRIPTION / METAL-BINDING / NEMO - IKK GAMMA - NFKB PATHWAY -DARPIN / TRANSCRIPTION REGULATION
Function / homology
Function and homology information


SLC15A4:TASL-dependent IRF5 activation / Modulation of host responses by IFN-stimulated genes / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / SUMOylation of immune response proteins / Regulation of NF-kappa B signaling / TNFR1-induced NF-kappa-B signaling pathway / RIP-mediated NFkB activation via ZBP1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation ...SLC15A4:TASL-dependent IRF5 activation / Modulation of host responses by IFN-stimulated genes / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / SUMOylation of immune response proteins / Regulation of NF-kappa B signaling / TNFR1-induced NF-kappa-B signaling pathway / RIP-mediated NFkB activation via ZBP1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / IkappaB kinase complex / Regulation of TNFR1 signaling / TRAF6 mediated NF-kB activation / Ovarian tumor domain proteases / IKK complex recruitment mediated by RIP1 / establishment of vesicle localization / linear polyubiquitin binding / PKR-mediated signaling / Activation of NF-kappaB in B cells / TAK1-dependent IKK and NF-kappa-B activation / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / Downstream TCR signaling / transferrin receptor binding / activated TAK1 mediates p38 MAPK activation / NOD1/2 Signaling Pathway / Ub-specific processing proteases / anoikis / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of T cell receptor signaling pathway / B cell homeostasis / positive regulation of macroautophagy / canonical NF-kappaB signal transduction / ubiquitin ligase complex / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / signaling adaptor activity / tumor necrosis factor-mediated signaling pathway / positive regulation of NF-kappaB transcription factor activity / spindle pole / mitotic spindle / protein-containing complex assembly / positive regulation of canonical NF-kappaB signal transduction / defense response to bacterium / protein heterodimerization activity / protein domain specific binding / DNA damage response / ubiquitin protein ligase binding / positive regulation of gene expression / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / zinc ion binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Nemo cc2-lz domain - 1d5 darpin complex / NF-kappa-B essential modulator NEMO, N-terminal / : / NF-kappa-B essential modulator NEMO / C2H2 type zinc-finger / NEMO, Zinc finger / Zinc finger CCHC NOA-type profile. / NF-kappa-B essential modulator NEMO, CC2-LZ domain / Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator / Ankyrin repeat-containing domain ...Nemo cc2-lz domain - 1d5 darpin complex / NF-kappa-B essential modulator NEMO, N-terminal / : / NF-kappa-B essential modulator NEMO / C2H2 type zinc-finger / NEMO, Zinc finger / Zinc finger CCHC NOA-type profile. / NF-kappa-B essential modulator NEMO, CC2-LZ domain / Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator / Ankyrin repeat-containing domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
NF-kappa-B essential modulator
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsGrubisha, O. / Duquerroy, S. / Cordier, F. / Haouz, A. / Delepierre, M. / Veron, M. / Agou, F.
Citation
Journal: J.Mol.Biol. / Year: 2010
Title: Darpin-Assisted Crystallography of the Cc2-Lz Domain of Nemo Reveals a Coupling between Dimerization and Ubiquitin-Binding.
Authors: Grubisha, O. / Kaminska, M. / Duquerroy, S. / Fontan, E. / Cordier, F. / Haouz, A. / Raynal, B. / Chiaravalli, J. / Delepierre, M. / Israel, A. / Veron, M. / Agou, F.
#1: Journal: Protein Sci. / Year: 2007
Title: Inhibition of NF-kappaB Activation with Designed Ankyrin-Repeat Proteins Targeting the Ubiquitin-Binding/Oligomerization Domain of Nemo.
Authors: Wyler, E. / Kaminska, M. / Coic, Y. / Baleux, F. / Veron, M. / Agou, F.
History
DepositionSep 22, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 21, 2016Group: Source and taxonomy / Structure summary
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NF-KAPPA-B ESSENTIAL MODULATOR
B: NF-KAPPA-B ESSENTIAL MODULATOR
C: 1D5 DARPIN
D: 1D5 DARPIN


Theoretical massNumber of molelcules
Total (without water)55,6404
Polymers55,6404
Non-polymers00
Water91951
1
A: NF-KAPPA-B ESSENTIAL MODULATOR
B: NF-KAPPA-B ESSENTIAL MODULATOR
C: 1D5 DARPIN
D: 1D5 DARPIN

A: NF-KAPPA-B ESSENTIAL MODULATOR
B: NF-KAPPA-B ESSENTIAL MODULATOR
C: 1D5 DARPIN
D: 1D5 DARPIN


Theoretical massNumber of molelcules
Total (without water)111,2818
Polymers111,2818
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area22000 Å2
ΔGint-173.5 kcal/mol
Surface area55160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.020, 63.020, 436.917
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13A
23B

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETTHRTHRAA251 - 29024 - 63
21METMETTHRTHRBB251 - 29024 - 63
12SERSERASNASNCC12 - 13612 - 136
22HISHISASNASNDD9 - 1369 - 136
13VALVALLYSLYSAA291 - 33764 - 110
23VALVALLYSLYSBB291 - 33764 - 110

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(-0.71226, -0.40316, 0.57458), (-0.13283, -0.72638, -0.67433), (0.68923, -0.55662, 0.46382)-19.1292, 215.30067, 100.09966
2given(-0.61081, -0.09723, 0.78579), (-0.44656, -0.77722, -0.44329), (0.65383, -0.62167, 0.43132)-76.43774, 188.6777, 110.26794
3given(-0.62225, -0.3231, 0.71303), (-0.23136, -0.79425, -0.56181), (0.74785, -0.51456, 0.41947)-50.05271, 202.21927, 102.71049

-
Components

#1: Protein NF-KAPPA-B ESSENTIAL MODULATOR / NF-KAPPA-B ESSENTIAL MODIFIER / INHIBITOR OF NUCLEAR FACTOR KAPPA-B KINASE SUBUNIT GAMMA / IKB ...NF-KAPPA-B ESSENTIAL MODIFIER / INHIBITOR OF NUCLEAR FACTOR KAPPA-B KINASE SUBUNIT GAMMA / IKB KINASE-ASSOCIATED PROTEIN 1 / NEMO


Mass: 12895.637 Da / Num. of mol.: 2 / Fragment: CC2-LZ DOMAIN, RESIDUES 251-337
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O88522
#2: Protein 1D5 DARPIN


Mass: 14924.489 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SEE SECONDARY REFERENCE / Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: PQE-30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1-BLUE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHAINS C AND D CORRESPOND TO GENBANK REFERENCE AY326425 OR GENPEPT REFERENCE AAQ93812. THE ...CHAINS C AND D CORRESPOND TO GENBANK REFERENCE AY326425 OR GENPEPT REFERENCE AAQ93812. THE MUTATIONS INTRODUCED IN CHAINS C AND D ARE DESCRIBED BELOW: DESIGNED DARPIN TARGETING NEMO CC2-LZ DOMAIN MUTATIONS 43N- 45R-46K-48N-56D-57Y-58D-69H- 76H-78N-79D-81S-89L-90F-102H

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.92 Å3/Da / Density % sol: 68.58 %
Description: THEORETICAL MODEL OF NEMO CC2 AND LZ HELICES USED FOR MOLECULAR REPLACEMENT
Crystal growpH: 7.5 / Details: 5% MPD, 5% ETHANOL, 100 MM HEPES, PH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.1741
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2007
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1741 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 86037 / % possible obs: 84.8 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.6
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.8 / % possible all: 42.9

-
Processing

Software
NameVersionClassification
REFMAC5.4.0069refinement
XDSdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JAB

2jab


Resolution: 2.9→47.67 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.889 / SU B: 31.453 / SU ML: 0.283 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.7 / ESU R Free: 0.377 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME RESIDUES COMING FROM THE TAG WERE VISIBLE IN THE DENSITY. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26821 883 4.9 %RANDOM
Rwork0.20754 ---
obs0.21051 17155 86.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.694 Å2
Baniso -1Baniso -2Baniso -3
1--1.66 Å20 Å20 Å2
2---1.66 Å20 Å2
3---3.33 Å2
Refinement stepCycle: LAST / Resolution: 2.9→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3491 0 0 51 3542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213532
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5861.9674752
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1395438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.43126.44191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.56515677
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7661515
X-RAY DIFFRACTIONr_chiral_restr0.1030.2533
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022673
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_it0.5621.52194
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.11123485
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.74231338
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0624.51267
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A156medium positional0.410.5
21C500medium positional0.320.5
31A188medium positional0.520.5
12B165loose positional1.065
22D449loose positional0.745
32B215loose positional0.925
11A156medium thermal0.392
21C500medium thermal2.112
31A188medium thermal1.232
12B165loose thermal0.6310
22D449loose thermal2.5910
32B215loose thermal2.610
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.42 31
Rwork0.298 680
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)
19.30510.46993.30573.15770.49587.9121-0.2021-0.30840.3086-0.13460.13120.2047-0.6922-1.36580.071-0.10930.24830.00450.21350.045-0.127714.18358.948172.355
22.48451.5493-0.77267.1782-2.28096.1966-0.04070.3828-0.1132-0.4670.0507-0.1598-0.0529-0.0027-0.0099-0.30020.07960.0129-0.2499-0.0303-0.099145.37655.578155.218
33.2862-2.62363.95635.6648-6.052516.4604-0.34310.03910.27520.17920.14250.0036-0.7008-0.47630.2005-0.10730.0552-0.06-0.245-0.0164-0.147532.95158.836167.609
46.9619-4.37648.48715.7053-7.046320.23110.09930.3587-0.3891-0.37130.19070.30270.1868-0.1409-0.2901-0.1798-0.0354-0.1115-0.1583-0.0876-0.136429.39653.93167.541
52.6765-2.68511.08712.9401-9.640454.83590.31550.0602-0.3083-0.70440.31350.24480.9186-0.3315-0.62890.38330.1618-0.04580.52780.1762-0.138252.45431.352223.39
66.0369-3.34576.77323.3287-5.878514.2959-0.05380.7380.3712-0.6973-0.8223-0.83680.50281.63240.87620.50160.2328-0.01810.61830.08080.058960.17833.285224.808
70.0131-0.14910.79481.7032-9.075548.3596-0.37610.5494-0.1931-0.76490.81620.5755-3.48322.3789-0.44010.51130.1037-0.0210.54490.2308-0.055258.78936.187245.338
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C12 - 136
2X-RAY DIFFRACTION2D9 - 136
3X-RAY DIFFRACTION3A291 - 337
4X-RAY DIFFRACTION4B291 - 337
5X-RAY DIFFRACTION5A251 - 290
6X-RAY DIFFRACTION6B247 - 290
7X-RAY DIFFRACTION7A240 - 250

+
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