[English] 日本語
Yorodumi
- PDB-5ulo: Crystal Structure of 14-3-3 zeta in Complex with a Serine 124-pho... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ulo
TitleCrystal Structure of 14-3-3 zeta in Complex with a Serine 124-phosphorylated TBC1D7 peptide
Components
  • 14-3-3 protein zeta/delta
  • TBC1 domain family member 7 peptide
KeywordsSIGNALING PROTEIN/peptide / 14-3-3 / TBC1D7 / phosphorylation / protein-peptide interaction / Structural Genomics / Structural Genomics Consortium / SGC / SIGNALING PROTEIN-peptide complex
Function / homology
Function and homology information


TSC1-TSC2 complex binding / TSC1-TSC2 complex / synaptic target recognition / Golgi reassembly / negative regulation of cilium assembly / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / response to growth factor / respiratory system process / regulation of synapse maturation ...TSC1-TSC2 complex binding / TSC1-TSC2 complex / synaptic target recognition / Golgi reassembly / negative regulation of cilium assembly / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / response to growth factor / respiratory system process / regulation of synapse maturation / tube formation / activation of GTPase activity / Rap1 signalling / negative regulation of TOR signaling / negative regulation of protein localization to nucleus / TBC/RABGAPs / KSRP (KHSRP) binds and destabilizes mRNA / GP1b-IX-V activation signalling / Regulation of localization of FOXO transcription factors / Interleukin-3, Interleukin-5 and GM-CSF signaling / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / regulation of ERK1 and ERK2 cascade / cellular response to glucose starvation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / positive regulation of GTPase activity / Transcriptional and post-translational regulation of MITF-M expression and activity / ERK1 and ERK2 cascade / GTPase activator activity / protein sequestering activity / negative regulation of innate immune response / hippocampal mossy fiber to CA3 synapse / cellular response to starvation / positive regulation of protein ubiquitination / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / Deactivation of the beta-catenin transactivating complex / lung development / Negative regulation of NOTCH4 signaling / regulation of protein stability / small GTPase binding / intracellular protein localization / melanosome / cytoplasmic vesicle / angiogenesis / DNA-binding transcription factor binding / vesicle / blood microparticle / transmembrane transporter binding / ciliary basal body / protein phosphorylation / cadherin binding / protein domain specific binding / lysosomal membrane / focal adhesion / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
TBC1 domain family member 7 / TBC1 domain family member 7, domain 2 / Rab-GTPase-TBC domain / Rab-GTPase-TBC domain superfamily / Rab-GTPase-TBC domain / TBC/rab GAP domain profile. / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site ...TBC1 domain family member 7 / TBC1 domain family member 7, domain 2 / Rab-GTPase-TBC domain / Rab-GTPase-TBC domain superfamily / Rab-GTPase-TBC domain / TBC/rab GAP domain profile. / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
14-3-3 protein zeta/delta / TBC1 domain family member 7 / TBC1 domain family member 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.14 Å
AuthorsDONG, A. / HU, J. / MADIGAN, J. / WALKER, J.R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / TONG, Y. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal Structure of 14-3-3 zeta in Complex with a Serine 124-phosphorylated TBC1D7 peptide
Authors: HU, J. / DONG, A. / MADIGAN, J. / WALKER, J.R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / TONG, Y. / Structural Genomics Consortium (SGC)
History
DepositionJan 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Sep 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_conn / struct_mon_prot_cis / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity_src_gen.gene_src_common_name / _pdbx_entity_src_syn.organism_common_name / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 2.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 14-3-3 protein zeta/delta
B: 14-3-3 protein zeta/delta
C: TBC1 domain family member 7 peptide
D: TBC1 domain family member 7 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,60714
Polymers58,4834
Non-polymers12410
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-24 kcal/mol
Surface area21610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.709, 71.575, 129.899
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein 14-3-3 protein zeta/delta / Protein kinase C inhibitor protein 1 / KCIP-1


Mass: 27834.143 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAZ / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R / References: UniProt: P63104
#2: Protein/peptide TBC1 domain family member 7 peptide


Mass: 1407.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q5SZL8, UniProt: Q9P0N9*PLUS
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 8 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG 3350, 0.2 M NaCl, 0.1 M HEPES pH7.5,5%~15% Ethylene Glycol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 36479 / % possible obs: 99.5 % / Redundancy: 8 % / Biso Wilson estimate: 59.73 Å2 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.023 / Rrim(I) all: 0.063 / Χ2: 2.214 / Net I/σ(I): 14.4 / Num. measured all: 291490
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.14-2.188.20.97918300.8390.3631.037100
2.18-2.228.30.730.9120.2681.0771000.778
2.22-2.268.20.6110.9320.2251.2651000.652
2.26-2.318.30.4590.970.1691.1451000.49
2.31-2.368.30.3970.9670.1461.1951000.423
2.36-2.418.30.3310.9760.1221.211000.353
2.41-2.478.30.2750.9810.1011.2621000.293
2.47-2.548.30.2160.9910.081.321000.231
2.54-2.618.30.180.9930.0671.3691000.193
2.61-2.78.20.1610.9920.061.6081000.172
2.7-2.798.30.140.9920.0521.8381000.149
2.79-2.98.20.1210.9920.0452.2261000.129
2.9-3.048.10.1050.9950.042.6191000.113
3.04-3.28.10.0830.9970.0312.9741000.089
3.2-3.480.0670.9980.0253.16699.90.071
3.4-3.667.80.060.9980.0233.69799.90.065
3.66-4.037.40.0560.9980.0224.51199.80.06
4.03-4.617.20.050.9980.024.64399.60.054
4.61-5.817.40.0440.9980.0173.75799.70.047
5.81-506.80.0360.9990.0153.26192.70.04

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.54 Å31.29 Å
Translation7.54 Å31.29 Å

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
BUSTER2.10.2refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A38

1a38


Resolution: 2.14→29.89 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.92 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.201 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.199 / SU Rfree Blow DPI: 0.182 / SU Rfree Cruickshank DPI: 0.184
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1101 3.03 %RANDOM
Rwork0.227 ---
obs0.228 36391 99.4 %-
Displacement parametersBiso max: 155.66 Å2 / Biso mean: 76.7 Å2 / Biso min: 28.92 Å2
Baniso -1Baniso -2Baniso -3
1--5.3721 Å20 Å20 Å2
2--9.4873 Å20 Å2
3----4.1152 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: final / Resolution: 2.14→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3573 0 32 60 3665
Biso mean--60.45 69.97 -
Num. residues----462
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1323SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes104HARMONIC2
X-RAY DIFFRACTIONt_gen_planes538HARMONIC5
X-RAY DIFFRACTIONt_it3701HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion494SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4403SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3701HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5007HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion2.69
X-RAY DIFFRACTIONt_other_torsion17.97
LS refinement shellResolution: 2.14→2.2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.302 106 3.64 %
Rwork0.267 2804 -
all0.268 2910 -
obs--98.41 %
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)
11.9205-0.3280.29993.04591.16852.5885-0.039-0.31780.6399-0.30280.1034-0.0731-0.4762-0.0878-0.0643-0.12230.00590.035-0.199-0.1129-0.050449.45210.22420.012
24.053-1.0994-0.02522.5311-0.61022.8050.1361-0.093-1.0559-0.196-0.1283-0.00640.69740.3231-0.0077-0.1180.0617-0.0233-0.33190.0237-0.020362.086-23.5949.847
32.9051-0.65870.14480.79070.34661.48460.03110.05760.1646-0.16970.0407-0.0424-0.00180.1063-0.07180.0373-0.02990.0731-0.0675-0.0246-0.02554.583-5.45410.195
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|229 }A1 - 229
2X-RAY DIFFRACTION2{ B|1 - B|229 }B1 - 229
3X-RAY DIFFRACTION3{ A|401 - A|430 C|301 - C|301 B|401 - B|427 D|301 - D|301 }A401 - 430
4X-RAY DIFFRACTION3{ A|401 - A|430 C|301 - C|301 B|401 - B|427 D|301 - D|301 }C301
5X-RAY DIFFRACTION3{ A|401 - A|430 C|301 - C|301 B|401 - B|427 D|301 - D|301 }B401 - 427
6X-RAY DIFFRACTION3{ A|401 - A|430 C|301 - C|301 B|401 - B|427 D|301 - D|301 }D301

+
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