[English] 日本語
Yorodumi
- PDB-3fx0: Crystal structure of Human NEMO CC2_LZ domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fx0
TitleCrystal structure of Human NEMO CC2_LZ domain
ComponentsNF-kappa-B essential modulator
KeywordsSIGNALING PROTEIN / Coiled-coil / Coiled coil / Cytoplasm / Disease mutation / Ectodermal dysplasia / Host-virus interaction / Metal-binding / Nucleus / Osteopetrosis / Phosphoprotein / Transcription / Transcription regulation / Ubl conjugation / Zinc / Zinc-finger
Function / homology
Function and homology information


IKBKB deficiency causes SCID / IKBKG deficiency causes anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID) (via TLR) / IkappaB kinase complex / establishment of vesicle localization / linear polyubiquitin binding / transferrin receptor binding / IkBA variant leads to EDA-ID / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / RIP-mediated NFkB activation via ZBP1 / positive regulation of ubiquitin-dependent protein catabolic process ...IKBKB deficiency causes SCID / IKBKG deficiency causes anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID) (via TLR) / IkappaB kinase complex / establishment of vesicle localization / linear polyubiquitin binding / transferrin receptor binding / IkBA variant leads to EDA-ID / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / RIP-mediated NFkB activation via ZBP1 / positive regulation of ubiquitin-dependent protein catabolic process / SUMOylation of immune response proteins / anoikis / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of T cell receptor signaling pathway / TRAF6 mediated NF-kB activation / positive regulation of macroautophagy / polyubiquitin modification-dependent protein binding / canonical NF-kappaB signal transduction / signaling adaptor activity / ubiquitin ligase complex / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TNFR1-induced NF-kappa-B signaling pathway / Regulation of NF-kappa B signaling / activated TAK1 mediates p38 MAPK activation / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / response to virus / PKR-mediated signaling / mitotic spindle / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / spindle pole / Interleukin-1 signaling / Ovarian tumor domain proteases / Downstream TCR signaling / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / ER-Phagosome pathway / protein-containing complex assembly / positive regulation of canonical NF-kappaB signal transduction / Ub-specific processing proteases / defense response to bacterium / inflammatory response / immune response / protein heterodimerization activity / protein domain specific binding / innate immune response / apoptotic process / ubiquitin protein ligase binding / DNA damage response / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Nemo cc2-lz domain - 1d5 darpin complex / C2H2 type zinc-finger / NF-kappa-B essential modulator NEMO, N-terminal / NF-kappa-B essential modulator NEMO / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
NF-kappa-B essential modulator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsLo, Y.C. / Lin, S.C. / Wu, H.
CitationJournal: Mol.Cell / Year: 2009
Title: Structural basis for recognition of diubiquitins by NEMO.
Authors: Lo, Y.C. / Lin, S.C. / Rospigliosi, C.C. / Conze, D.B. / Wu, C.J. / Ashwell, J.D. / Eliezer, D. / Wu, H.
History
DepositionJan 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: NF-kappa-B essential modulator
B: NF-kappa-B essential modulator


Theoretical massNumber of molelcules
Total (without water)22,1492
Polymers22,1492
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-37 kcal/mol
Surface area10090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.194, 76.194, 76.892
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein NF-kappa-B essential modulator / NEMO / NF-kappa-B essential modifier / Inhibitor of nuclear factor kappa-B kinase subunit gamma / ...NEMO / NF-kappa-B essential modifier / Inhibitor of nuclear factor kappa-B kinase subunit gamma / IkB kinase subunit gamma / I-kappa-B kinase gamma / IKK-gamma / IKKG / IkB kinase-associated protein 1 / IKKAP1 / FIP-3


Mass: 11074.619 Da / Num. of mol.: 2 / Fragment: CC2_LZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IKBKG, FIP3, NEMO / Plasmid: pET-28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL / References: UniProt: Q9Y6K9

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10% PEG 1000, 10% PEG 4000, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM Q315r / Detector: CCD / Date: Aug 3, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionRedundancy: 9.6 % / Av σ(I) over netI: 24.54 / Number: 72528 / Rmerge(I) obs: 0.063 / Χ2: 1 / D res high: 3.3 Å / D res low: 50 Å / Num. obs: 7530 / % possible obs: 99.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.15096.610.0390.898.9
5.647.199.510.0621.1259.4
4.935.6499.710.0681.1129.5
4.484.9399.610.0660.9839.7
4.164.4899.710.0860.9659.8
3.914.1699.710.0990.9179.8
3.723.9199.610.1541.0099.8
3.553.7299.610.2641.0739.8
3.423.5599.610.4490.9689.8
3.33.4299.610.60.9799.8
ReflectionResolution: 3.19→32.99 Å / Num. all: 4240 / Num. obs: 4241 / % possible obs: 99 % / Observed criterion σ(F): 0 / Redundancy: 5.4 % / Limit h max: 20 / Limit h min: 1 / Limit k max: 20 / Limit k min: 1 / Limit l max: 23 / Limit l min: 0 / Observed criterion F max: 376726.54 / Observed criterion F min: 0.55 / Rmerge(I) obs: 0.058 / Χ2: 0.863
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.2-3.45.60.5466980.60699.4
3.4-3.665.50.2697070.70499.6
3.66-4.035.50.1077140.91399.7
4.03-4.615.50.0686980.93799.6
4.61-5.815.40.0597100.93299.6
5.81-354.90.0397141.1296.5

-
Phasing

PhasingMethod: SAD
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
165.65817.1019.463S201
262.02913.6286.669S200.769
379.13229.753-15.861S200.518
477.57332.619-12.253S200.487
547.613.73621.693S200.386
685.30922.8430.168S200.367
760.75930.3279.571S200.304
873.77521.022-20.925S200.296

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
CNS1.2refinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 3.2→35 Å / Rfactor Rfree error: 0.015 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.306 431 10.2 %RANDOM
Rwork0.247 ---
all-4239 --
obs-4105 96.8 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 123.734 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 200 Å2 / Biso mean: 150.224 Å2 / Biso min: 59.19 Å2
Baniso -1Baniso -2Baniso -3
1-16.526 Å20 Å20 Å2
2--16.526 Å20 Å2
3----33.052 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.69 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a1.06 Å0.76 Å
Luzzati d res high-3.2
Refinement stepCycle: LAST / Resolution: 3.2→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1088 0 0 0 1088
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_torsion_deg23
X-RAY DIFFRACTIONx_torsion_impr_deg0.72
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
3.2-3.350.4254710.10.4134190.06252346689.1
3.35-3.520.4325110.30.3414450.06152549694.5
3.52-3.740.365911.50.3024550.04752851497.3
3.74-4.030.324509.60.2284720.04653652297.4
4.03-4.440.3426612.70.2394520.04252151899.4
4.44-5.080.36712.50.2334680.03753653599.8
5.08-6.390.314509.40.2694800.04453253099.6
6.39-32.990.231417.80.2164830.03654052497
Xplor fileSerial no: 1 / Param file: CNS_TOPPAR:protein_rep.param

+
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://pdbjlvh1.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