[English] 日本語
Yorodumi
- PDB-3zmf: Salmonella enterica SadA 303-358 fused to GCN4 adaptors (SadAK2) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zmf
TitleSalmonella enterica SadA 303-358 fused to GCN4 adaptors (SadAK2)
ComponentsGENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN, GENERAL CONTROL PROTEIN GCN4
KeywordsMEMBRANE PROTEIN / DALL DOMAIN / DALL2 / TAA
Function / homology
Function and homology information


FCERI mediated MAPK activation / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / mediator complex binding / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / amino acid biosynthetic process ...FCERI mediated MAPK activation / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / mediator complex binding / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / amino acid biosynthetic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription initiation by RNA polymerase II / cellular response to nutrient levels / cellular response to amino acid starvation / cell outer membrane / RNA polymerase II transcription regulator complex / protein transport / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / cell surface / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus
Similarity search - Function
Trimeric autotransporter adhesin YadA-like, head domain / YadA head domain repeat (2 copies) / ESPR domain / Extended Signal Peptide of Type V secretion system / Trimeric autotransporter adhesin YadA-like, stalk domain / Coiled stalk of trimeric autotransporter adhesin / Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain / YadA-like membrane anchor domain / : / Serralysin-like metalloprotease, C-terminal ...Trimeric autotransporter adhesin YadA-like, head domain / YadA head domain repeat (2 copies) / ESPR domain / Extended Signal Peptide of Type V secretion system / Trimeric autotransporter adhesin YadA-like, stalk domain / Coiled stalk of trimeric autotransporter adhesin / Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain / YadA-like membrane anchor domain / : / Serralysin-like metalloprotease, C-terminal / Pilin-like / Basic region leucine zipper / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily
Similarity search - Domain/homology
General control transcription factor GCN4 / Autotransporter adhesin SadA
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsHartmann, M.D. / Hernandez Alvarez, B. / Albrecht, R. / Lupas, A.N.
Citation
Journal: Protein Eng.Des.Sel. / Year: 2008
Title: A New Expression System for Protein Crystallization Using Trimeric Coiled-Coil Adaptors.
Authors: Hernandez Alvarez, B. / Hartmann, M.D. / Albrecht, R. / Lupas, A.N. / Zeth, K. / Linke, D.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Complete Fiber Structures of Complex Trimeric Autotransporter Adhesins Conserved in Enterobacteria.
Authors: Hartmann, M.D. / Grin, I. / Dunin-Horkawicz, S. / Deiss, S. / Linke, D. / Lupas, A.N. / Hernandez Alvarez, B.
History
DepositionFeb 8, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Source and taxonomy
Revision 1.2Dec 20, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN, GENERAL CONTROL PROTEIN GCN4
B: GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN, GENERAL CONTROL PROTEIN GCN4
C: GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN, GENERAL CONTROL PROTEIN GCN4


Theoretical massNumber of molelcules
Total (without water)37,4473
Polymers37,4473
Non-polymers00
Water2,216123
1
C: GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN, GENERAL CONTROL PROTEIN GCN4

C: GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN, GENERAL CONTROL PROTEIN GCN4

C: GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN, GENERAL CONTROL PROTEIN GCN4


Theoretical massNumber of molelcules
Total (without water)37,4473
Polymers37,4473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_355-x+y-2,-x,z1
crystal symmetry operation2_575-y,x-y+2,z1
Buried area13180 Å2
ΔGint-150.7 kcal/mol
Surface area16570 Å2
MethodPISA
2
B: GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN, GENERAL CONTROL PROTEIN GCN4

B: GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN, GENERAL CONTROL PROTEIN GCN4

B: GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN, GENERAL CONTROL PROTEIN GCN4


Theoretical massNumber of molelcules
Total (without water)37,4473
Polymers37,4473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area13400 Å2
ΔGint-145.7 kcal/mol
Surface area16460 Å2
MethodPISA
3
A: GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN, GENERAL CONTROL PROTEIN GCN4

A: GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN, GENERAL CONTROL PROTEIN GCN4

A: GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN, GENERAL CONTROL PROTEIN GCN4


Theoretical massNumber of molelcules
Total (without water)37,4473
Polymers37,4473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area13260 Å2
ΔGint-140 kcal/mol
Surface area16820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.590, 46.590, 128.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-2002-

HOH

21A-2025-

HOH

31B-2015-

HOH

41B-2039-

HOH

51C-2009-

HOH

61C-2025-

HOH

-
Components

#1: Protein GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN, GENERAL CONTROL PROTEIN GCN4 / AMINO ACID BIOSYNTHESIS REGULATORY PROTEIN / AUTOTRANSPORTER ADHESIN FRAGMENT


Mass: 12482.168 Da / Num. of mol.: 3
Fragment: GCN4 ADAPTOR RESIDUES 250-278, ADHESIN RESIDUES 303-358, GCN4 ADAPTOR RESIDUES 250-278
Mutation: YES
Source method: isolated from a genetically manipulated source
Details: N- AND C-TERMINAL IN-REGISTER FUSION TO GCN4 ADAPTORS
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast), (gene. exp.) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03069, UniProt: Q8ZL64
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growDetails: 50% PEG 200, 0.1 M NA-CITRATE PH 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9686
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 31, 2007
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.726
11K, H, -L20.274
ReflectionResolution: 1.85→38.5 Å / Num. obs: 26591 / % possible obs: 99.2 % / Redundancy: 3.72 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.2
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 3.15 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.9 / % possible all: 97.4

-
Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GCM

1gcm


Resolution: 1.85→38.51 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.911 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.22051 1316 4.9 %RANDOM
Rwork0.18135 ---
obs0.18325 25273 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.523 Å2
Baniso -1Baniso -2Baniso -3
1-15.21 Å20 Å20 Å2
2--15.21 Å20 Å2
3----30.42 Å2
Refinement stepCycle: LAST / Resolution: 1.85→38.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2422 0 0 123 2545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0192448
X-RAY DIFFRACTIONr_bond_other_d0.0040.022355
X-RAY DIFFRACTIONr_angle_refined_deg2.1471.9553327
X-RAY DIFFRACTIONr_angle_other_deg1.06435398
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9085332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.75427.24187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.23515424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.793152
X-RAY DIFFRACTIONr_chiral_restr0.1440.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022788
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02472
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
LS refinement shellResolution: 1.849→1.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 98 -
Rwork0.21 1789 -
obs--95.3 %
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)
10.3907-0.16-1.3033.117-4.488314.1742-0.09550.0213-0.17440.2359-0.2734-0.07210.1750.90010.36890.2038-0.0093-0.0780.3761-0.07090.25314.683-2.887-53.557
20.1050.1759-0.82860.3576-1.381815.2602-0.04930.0156-0.0152-0.059-0.0407-0.0538-0.41440.510.090.17240.0196-0.01610.24850.01350.1025-17.8612.719-33.692
30.1148-0.1974-0.7351.234-1.104913.8419-0.08220.0576-0.0665-0.0743-0.21770.11130.4799-0.1790.30.2136-0.02050.05860.2372-0.04490.0717-47.10921.63692.936
40.564-0.55122.11991.3263-0.527217.93730.03470.1669-0.1301-0.1097-0.09510.0448-0.2488-0.12620.06040.19980.0118-0.01070.1888-0.09430.1732-0.05-5.985-24.115
52.5302-1.3629-0.01711.0892-2.215613.9414-0.01420.1362-0.00480.0125-0.0522-0.0101-0.0228-0.1330.06630.0876-0.0091-0.00320.033-0.01320.1783-20.4318.102-3.414
62.1823-1.2741-4.36760.84853.402620.2399-0.1925-0.22860.07250.11970.0102-0.02420.07570.30540.18230.127-0.0486-0.03190.272-0.01330.1384-41.44923.8863.038
71.23820.04580.33180.4949-0.08370.64140.01430.0689-0.0307-0.04480.03610.0344-0.0017-0.0383-0.05050.03050.00750.00150.01370.00740.1866-1.497-0.567-2.377
80.5738-0.06380.29431.10650.1740.62920.0075-0.0059-0.02590.039-0.00610.02830.0038-0.0382-0.00140.00660.00430.00560.0151-0.00050.1634-24.14612.12718.264
90.42270.01570.07180.76530.35021.25340.02220.0060.05510.0129-0.0015-0.02390.01650.0107-0.02070.0320.0089-0.00090.03810.00340.1755-45.46928.03841.5
100.59960.1616-2.24340.3101-0.923110.4337-0.0584-0.0339-0.02820.0435-0.0380.00340.17050.05340.09630.07240.00230.01190.01290.0030.20862.767-4.99631.837
110.30520.0322-0.19410.7692-2.141511.8623-0.0497-0.0958-0.08310.0871-0.040.00830.01160.19880.08960.06290.01070.00010.09240.01470.191-18.22411.63752.441
120.58920.195-1.29680.7244-1.065710.551-0.02170.06510.0269-0.0332-0.05190.01190.0694-0.02190.07360.01860.01510.00420.02850.00770.1859-43.4722.0676.972
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A277 - 303
2X-RAY DIFFRACTION2B277 - 303
3X-RAY DIFFRACTION3C277 - 303
4X-RAY DIFFRACTION4A304 - 317
5X-RAY DIFFRACTION5B304 - 317
6X-RAY DIFFRACTION6C304 - 317
7X-RAY DIFFRACTION7A318 - 358
8X-RAY DIFFRACTION8B318 - 358
9X-RAY DIFFRACTION9C318 - 358
10X-RAY DIFFRACTION10A359 - 387
11X-RAY DIFFRACTION11B359 - 387
12X-RAY DIFFRACTION12C359 - 387

+
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