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- PDB-4lmg: Crystal structure of AFT2 in complex with DNA -

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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 selenite ion / iron-sulfur cluster binding / cellular response to oxidative stress / DNA-binding transcription activator activity, RNA polymerase II-specific / intracellular iron ion homeostasis / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding ...: / regulation of phosphate transmembrane transport / cardiolipin metabolic process / cellular response to selenite ion / iron-sulfur cluster binding / cellular response to oxidative stress / DNA-binding transcription activator activity, RNA polymerase II-specific / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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