[English] 日本語
Yorodumi
- PDB-4lmg: Crystal structure of AFT2 in complex with DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lmg
TitleCrystal structure of AFT2 in complex with DNA
Components
  • 5'-D(*AP*AP*GP*TP*GP*CP*AP*CP*CP*CP*AP*TP*T)-3'
  • 5'-D(*TP*AP*AP*TP*GP*GP*GP*TP*GP*CP*AP*CP*T)-3'
  • Iron-regulated transcriptional activator AFT2
KeywordsTRANSCRIPTION ACTIVATOR/DNA / WRKY-GCM1 / TRANSCRIPTION FACTOR / DNA BINDING / IRON BINDING / TRANSCRIPTION ACTIVATOR-DNA COMPLEX / WRKY-GCM1 fold
Function / homology
Function and homology information


regulation of phosphate transmembrane transport / cardiolipin metabolic process / cellular response to iron ion starvation / iron-sulfur cluster binding / intracellular iron ion homeostasis / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleus
Similarity search - Function
Iron-regulated transcriptional activator AFT / Transcription factor AFT
Similarity search - Domain/homology
DNA / DNA (> 10) / Iron-regulated transcriptional activator AFT2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsPoor, C.B. / Sanishvili, R. / Schuermann, J.P. / He, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Molecular mechanism and structure of the Saccharomyces cerevisiae iron regulator Aft2.
Authors: Poor, C.B. / Wegner, S.V. / Li, H. / Dlouhy, A.C. / Schuermann, J.P. / Sanishvili, R. / Hinshaw, J.R. / Riggs-Gelasco, P.J. / Outten, C.E. / He, C.
History
DepositionJul 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Iron-regulated transcriptional activator AFT2
B: Iron-regulated transcriptional activator AFT2
C: Iron-regulated transcriptional activator AFT2
D: Iron-regulated transcriptional activator AFT2
E: 5'-D(*TP*AP*AP*TP*GP*GP*GP*TP*GP*CP*AP*CP*T)-3'
F: 5'-D(*AP*AP*GP*TP*GP*CP*AP*CP*CP*CP*AP*TP*T)-3'
G: 5'-D(*TP*AP*AP*TP*GP*GP*GP*TP*GP*CP*AP*CP*T)-3'
H: 5'-D(*AP*AP*GP*TP*GP*CP*AP*CP*CP*CP*AP*TP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,40514
Polymers89,0138
Non-polymers3926
Water4,558253
1
A: Iron-regulated transcriptional activator AFT2
D: Iron-regulated transcriptional activator AFT2
G: 5'-D(*TP*AP*AP*TP*GP*GP*GP*TP*GP*CP*AP*CP*T)-3'
H: 5'-D(*AP*AP*GP*TP*GP*CP*AP*CP*CP*CP*AP*TP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7037
Polymers44,5064
Non-polymers1963
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-47 kcal/mol
Surface area18030 Å2
MethodPISA
2
B: Iron-regulated transcriptional activator AFT2
C: Iron-regulated transcriptional activator AFT2
E: 5'-D(*TP*AP*AP*TP*GP*GP*GP*TP*GP*CP*AP*CP*T)-3'
F: 5'-D(*AP*AP*GP*TP*GP*CP*AP*CP*CP*CP*AP*TP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7037
Polymers44,5064
Non-polymers1963
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-47 kcal/mol
Surface area18120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.536, 127.453, 70.766
Angle α, β, γ (deg.)90.00, 90.04, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Iron-regulated transcriptional activator AFT2 / Activator of iron transcription protein 2


Mass: 18282.133 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 38-193
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288C / Gene: AFT2, YPL202C / Production host: Escherichia coli (E. coli) / References: UniProt: Q08957
#2: DNA chain 5'-D(*TP*AP*AP*TP*GP*GP*GP*TP*GP*CP*AP*CP*T)-3'


Mass: 4006.621 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: PROMOTER REGION FRAGMENT
#3: DNA chain 5'-D(*AP*AP*GP*TP*GP*CP*AP*CP*CP*CP*AP*TP*T)-3'


Mass: 3935.587 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: PROMOTER REGION FRAGMENT
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 41.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 23% PEG2000 MME, 0.2 M MAGNESIUM CHLORIDE, 0.1 M BIS-TRIS, PH 6.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.28162 / Wavelength: 1.28162 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 7, 2011
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28162 Å / Relative weight: 1
ReflectionResolution: 2.2→19.931 Å / Num. obs: 36252 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 7.5 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 16.5
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 3.6 / % possible all: 100

-
Processing

Software
NameVersionClassification
XDSdata scaling
PHENIXmodel building
PHENIX(PHENIX.REFINE: 1.6.4_486)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→19.93 Å / SU ML: 0.32 / σ(F): 0.19 / Phase error: 26.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1953 5.39 %random
Rwork0.189 ---
obs0.192 36218 97.3 %-
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.91 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.2617 Å2-0 Å2-0.4644 Å2
2---9.5208 Å20 Å2
3---16.7825 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4053 1036 6 253 5348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035327
X-RAY DIFFRACTIONf_angle_d0.6827397
X-RAY DIFFRACTIONf_dihedral_angle_d17.1462090
X-RAY DIFFRACTIONf_chiral_restr0.043809
X-RAY DIFFRACTIONf_plane_restr0.002757
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2550.29221320.25252273X-RAY DIFFRACTION93
2.255-2.31590.28941330.22712374X-RAY DIFFRACTION93
2.3159-2.38390.28431340.2222366X-RAY DIFFRACTION95
2.3839-2.46070.27261370.21312408X-RAY DIFFRACTION95
2.4607-2.54850.28031370.22292387X-RAY DIFFRACTION95
2.5485-2.65030.35121420.23992448X-RAY DIFFRACTION97
2.6503-2.77060.31011410.24012447X-RAY DIFFRACTION98
2.7706-2.91630.28441410.2162497X-RAY DIFFRACTION98
2.9163-3.09840.2491400.21762460X-RAY DIFFRACTION99
3.0984-3.33660.25061400.19242487X-RAY DIFFRACTION99
3.3366-3.67040.21851390.16742500X-RAY DIFFRACTION99
3.6704-4.19720.20541460.16532546X-RAY DIFFRACTION100
4.1972-5.27180.16741470.14232518X-RAY DIFFRACTION100
5.2718-19.93170.20531440.17832554X-RAY DIFFRACTION100
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)
11.21-0.530.26252.45680.29581.87090.02320.0891-0.01140.03940.0376-0.05040.1761-0.1218-0.06810.1329-0.00550.00760.16720.05950.2635.234463.968328.3803
21.92390.5205-0.09793.9881-1.52860.7494-0.1283-0.03590.04060.17480.10710.12250.1176-0.03050.01040.16530.02510.00080.1765-0.11240.15985.435842.72670.5992
31.8333-0.6679-0.27872.80550.06381.2285-0.0307-0.02250.1987-0.1010.1417-0.1418-0.0971-0.07-0.10550.142-0.011-0.01010.1466-0.00770.168714.544981.8376.5225
42.00280.5663-0.42752.3873-0.10470.5927-0.18830.00040.1433-0.0750.1027-0.0548-0.1462-0.02080.07350.1647-0.0045-0.01210.1323-0.04920.10426.1685102.965534.7086
54.0421.48980.13681.4080.3464-0.0289-0.54520.6039-0.1585-0.09530.3509-0.12660.00450.08430.12830.1702-0.00580.00930.2766-0.08620.240917.76363.3666-0.3642
63.8972-1.4198-0.44331.47390.34320.2093-0.5562-0.3323-0.29260.03750.28610.11410.1572-0.0940.16160.0731-0.02140.03210.162-0.00470.170323.682182.620435.452
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E and chain F
6X-RAY DIFFRACTION6chain G and chain H

+
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