[English] 日本語
Yorodumi
- PDB-4chk: Crystal Structure of the ARF5 oligomerization domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4chk
TitleCrystal Structure of the ARF5 oligomerization domain
ComponentsAUXIN RESPONSE FACTOR 5
KeywordsTRANSCRIPTION / PB1
Function / homology
Function and homology information


meristem development / longitudinal axis specification / xylem and phloem pattern formation / leaf vascular tissue pattern formation / root development / response to auxin / flower development / auxin-activated signaling pathway / embryo development ending in seed dormancy / transcription cis-regulatory region binding ...meristem development / longitudinal axis specification / xylem and phloem pattern formation / leaf vascular tissue pattern formation / root development / response to auxin / flower development / auxin-activated signaling pathway / embryo development ending in seed dormancy / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / identical protein binding / nucleus
Similarity search - Function
Auxin response factor domain / Auxin response factor / Auxin response factor / AUX/IAA domain / AUX/IAA family / B3 DNA binding domain / B3 DNA binding domain / B3 DNA-binding domain profile. / B3 DNA binding domain / DNA-binding pseudobarrel domain superfamily ...Auxin response factor domain / Auxin response factor / Auxin response factor / AUX/IAA domain / AUX/IAA family / B3 DNA binding domain / B3 DNA binding domain / B3 DNA-binding domain profile. / B3 DNA binding domain / DNA-binding pseudobarrel domain superfamily / PB1 domain profile. / PB1 domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Auxin response factor 5
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.85 Å
AuthorsNanao, M.H. / Mazzoleni, M. / Thevenon, E. / Brunoud, G. / Vernoux, T. / Parcy, F. / Dumas, R.
CitationJournal: Nat.Commun. / Year: 2014
Title: Structural Basis for Oligomerisation of Auxin Transcriptional Regulators
Authors: Nanao, M.H. / Vinos-Poyo, T. / Brunoud, G. / Thevenon, E. / Mazzoleni, M. / Mast, D. / Laine, S. / Wang, S. / Hagen, G. / Li, H. / Guilfoyle, T.J. / Parcy, F. / Vernoux, T. / Dumas, R.
History
DepositionDec 3, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AUXIN RESPONSE FACTOR 5
B: AUXIN RESPONSE FACTOR 5
C: AUXIN RESPONSE FACTOR 5
D: AUXIN RESPONSE FACTOR 5
E: AUXIN RESPONSE FACTOR 5
F: AUXIN RESPONSE FACTOR 5
G: AUXIN RESPONSE FACTOR 5
H: AUXIN RESPONSE FACTOR 5


Theoretical massNumber of molelcules
Total (without water)112,6888
Polymers112,6888
Non-polymers00
Water2,864159
1
A: AUXIN RESPONSE FACTOR 5
E: AUXIN RESPONSE FACTOR 5


Theoretical massNumber of molelcules
Total (without water)28,1722
Polymers28,1722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-9.3 kcal/mol
Surface area14090 Å2
MethodPQS
2
B: AUXIN RESPONSE FACTOR 5
D: AUXIN RESPONSE FACTOR 5


Theoretical massNumber of molelcules
Total (without water)28,1722
Polymers28,1722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-7.2 kcal/mol
Surface area11910 Å2
MethodPQS
3
C: AUXIN RESPONSE FACTOR 5
F: AUXIN RESPONSE FACTOR 5


Theoretical massNumber of molelcules
Total (without water)28,1722
Polymers28,1722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-4.1 kcal/mol
Surface area12270 Å2
MethodPQS
4
H: AUXIN RESPONSE FACTOR 5

D: AUXIN RESPONSE FACTOR 5


Theoretical massNumber of molelcules
Total (without water)28,1722
Polymers28,1722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x+1/2,y-1/2,-z1
5
G: AUXIN RESPONSE FACTOR 5

F: AUXIN RESPONSE FACTOR 5


Theoretical massNumber of molelcules
Total (without water)28,1722
Polymers28,1722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556-x+1/2,y+1/2,-z+11
6
G: AUXIN RESPONSE FACTOR 5

B: AUXIN RESPONSE FACTOR 5


Theoretical massNumber of molelcules
Total (without water)28,1722
Polymers28,1722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)196.264, 86.438, 91.371
Angle α, β, γ (deg.)90.00, 112.71, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.2377, -0.8586, -0.4542), (-0.1659, -0.4967, 0.8519), (-0.9571, -0.1272, -0.2605)73.4224, 4.4159, 21.8426
2given(-0.2846, 0.5523, -0.7836), (0.9586, 0.1636, -0.2329), (-0.0004, -0.8174, -0.576)76.3148, -29.9313, 44.0567
3given(-0.2196, -0.9721, -0.0824), (-0.5133, 0.0433, 0.8571), (-0.8297, 0.2305, -0.5085)79.0377, 3.4112, 75.1284
4given(0.7946, 0.4602, 0.396), (-0.5807, 0.7663, 0.2748), (-0.177, -0.4483, 0.8762)7.7122, 15.7668, -15.8001
5given(0.1938, 0.2227, -0.9554), (0.8934, -0.4424, 0.0781), (-0.4052, -0.8688, -0.2847)73.217, -37.6059, 23.3201
6given(-0.4136, -0.3739, 0.8301), (-0.4415, -0.715, -0.5421), (0.7962, -0.5907, 0.1306)30.1124, 55.3111, -26.391
7given(0.7619, -0.6324, -0.1399), (0.4928, 0.7061, -0.5085), (0.4204, 0.3184, 0.8496)0.3592, -25.2307, 6.1533

-
Components

#1: Protein
AUXIN RESPONSE FACTOR 5 / AUXIN-RESPONSIVE PROTEIN IAA24 / TRANSCRIPTION FACTOR MONOPTEROS / AUXIN RESPONSE FACTOR 5 ARF5


Mass: 14085.997 Da / Num. of mol.: 8 / Fragment: RESIDUES 779-902
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P93024
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 3.17 Å3/Da / Density % sol: 61.23 % / Description: NONE
Crystal growpH: 8 / Details: 12% DIOXANE, pH 8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 26, 2012 / Details: KB
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.84→50 Å / Num. obs: 33135 / % possible obs: 99.1 % / Observed criterion σ(I): -1 / Redundancy: 3.7 % / Biso Wilson estimate: 98.32 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.37
Reflection shellResolution: 2.84→3.01 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.89 / % possible all: 96.5

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
SHARPphasing
SHELXDphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.85→45.26 Å / Cor.coef. Fo:Fc: 0.9376 / Cor.coef. Fo:Fc free: 0.9235 / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE ELECTRON DENSITY FOR THE D, E, F, G AND H IS POOR AND RESIDUES 62-64 WERE OMITTED FROM CHAINS F,G AND H THE DENSITY FOR THE C-TERMINAL HELIX WAS OF GOOD QUALITY IN SUBUNIT A, BUT POOR ...Details: THE ELECTRON DENSITY FOR THE D, E, F, G AND H IS POOR AND RESIDUES 62-64 WERE OMITTED FROM CHAINS F,G AND H THE DENSITY FOR THE C-TERMINAL HELIX WAS OF GOOD QUALITY IN SUBUNIT A, BUT POOR FOR THE REMAINING SUBUNITS, ESPECIALLY TOWARDS THE END OF THE MODELLED HELIX. HOWEVER, IN SUBUNIT E, BROKEN AND POORLY DEFINED HELICAL DENSITY EXTENDED FURTHER AND WAS MODELLED AS RESIDUES LYS 112 TO ILE 119, BUT INTERPRETATION OF THIS REGION SHOULD BE DONE WITH CARE BECAUSE OF THE QUALITY OF THE ELECTRON DENSITY. SIMILARLY, IN SUBUNIT H, RESIDUES GLY 110 TO ASP121 WERE ORDERED AND VISIBLE, PROBABLY BECAUSE THIS SEGMENT MAKES CRYSTAL CONTACTS WITH SUBUNIT C AND F.
RfactorNum. reflection% reflectionSelection details
Rfree0.2205 1725 5.22 %RANDOM
Rwork0.1823 ---
obs0.1843 33076 --
Displacement parametersBiso mean: 88.56 Å2
Baniso -1Baniso -2Baniso -3
1-14.2794 Å20 Å2-2.9066 Å2
2--1.9208 Å20 Å2
3----16.2002 Å2
Refine analyzeLuzzati coordinate error obs: 0.504 Å
Refinement stepCycle: LAST / Resolution: 2.85→45.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5937 0 0 159 6096
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016063HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.228193HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2137SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes158HARMONIC2
X-RAY DIFFRACTIONt_gen_planes853HARMONIC5
X-RAY DIFFRACTIONt_it6063HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.87
X-RAY DIFFRACTIONt_other_torsion21.29
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion773SEMIHARMONIC5
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_contact6487SEMIHARMONIC4
LS refinement shellResolution: 2.85→2.94 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.342 148 5.22 %
Rwork0.2543 2688 -
all0.259 2836 -
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)
15.63130.51640.56683.4737-0.32362.71880.2679-0.0831-0.49620.2868-0.3091-0.00850.0150.26090.0411-0.1367-0.13120.0507-0.1484-0.0064-0.146552.1614-11.694328.3651
26.11262.07180.32514.34280.50544.8764-0.0468-0.12860.0035-0.02610.065-0.5185-0.20190.1126-0.0182-0.1562-0.253-0.006-0.178-0.0178-0.108173.00864.38821.7354
35.2035-1.49551.05434.07020.40865.6707-0.00970.2025-0.0583-0.1434-0.02960.1481-0.8063-0.69270.0393-0.05830.03990.167-0.1763-0.0703-0.192424.51243.497422.7801
47.29111.05710.89226.8974-2.033.1368-0.26220.5330.4630.57720.40660.14-0.359-0.2208-0.1444-0.0343-0.18420.0515-0.21650.1074-0.186752.122413.453113.5148
52.57852.825-1.22865.9438-3.73119.7048-0.0015-0.02350.16850.67380.01110.3337-0.4816-0.3331-0.00950.0666-0.20150.0905-0.13680.0547-0.169343.3692-21.02348.6311
64.59544.509-0.300112.32881.43614.79310.24910.129-1.0820.2671-0.4287-0.85830.0936-0.36770.1797-0.3502-0.2230.0543-0.2108-0.17010.088817.9958-20.238519.4152
79.3955-2.9797-1.38386.8178-1.07214.1430.29380.255-0.7183-0.57330.00360.34730.0787-0.4184-0.2975-0.3130.2740.0405-0.16260.13250.065762.90316.812462.9474
80.76630.7781-0.98391.70761.53225.04070.33470.3343-0.4473-0.3502-0.22510.09990.10290.8184-0.1097-0.21730.1356-0.02830.0244-0.2138-0.117454.2375-16.56125.0147
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESSEQ 18:115
2X-RAY DIFFRACTION2CHAIN B AND RESSEQ 19:110
3X-RAY DIFFRACTION3CHAIN C AND RESSEQ 18:109
4X-RAY DIFFRACTION4CHAIN D AND RESSEQ 18:109
5X-RAY DIFFRACTION5CHAIN E AND { RESSEQ 18:108 OR RESSEQ 111:119 }
6X-RAY DIFFRACTION6CHAIN F AND RESSEQ 18:108
7X-RAY DIFFRACTION7CHAIN G AND { RESSEQ 18:61 OR RESSEQ 65:108 }
8X-RAY DIFFRACTION8CHAIN H AND { RESSEQ 18:61 OR RESSEQ 65:106 OR RESSEQ 110:121 }

+
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