[English] 日本語
Yorodumi
- PDB-3nmn: Crystal structure of pyrabactin-bound abscisic acid receptor PYL1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3nmn
TitleCrystal structure of pyrabactin-bound abscisic acid receptor PYL1 in complex with type 2C protein phosphatase ABI1
Components
  • Abscisic acid receptor PYL1
  • Protein phosphatase 2C 56
KeywordsPROTEIN BINDING / PYL1 / Pyrabactin / Plant hormone receptor / abscisic acid signaling
Function / homology
Function and homology information


regulation of abscisic acid-activated signaling pathway / negative regulation of abscisic acid-activated signaling pathway / : / protein phosphatase inhibitor complex / regulation of stomatal movement / response to abscisic acid / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / plastid ...regulation of abscisic acid-activated signaling pathway / negative regulation of abscisic acid-activated signaling pathway / : / protein phosphatase inhibitor complex / regulation of stomatal movement / response to abscisic acid / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / plastid / protein serine/threonine phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / phosphatase activity / phosphoprotein phosphatase activity / protein dephosphorylation / response to cold / kinase binding / defense response / signaling receptor activity / response to heat / protein kinase binding / protein homodimerization activity / identical protein binding / nucleus / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
PPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain signature. / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / Protein phosphatase 2C / Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. ...PPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain signature. / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / Protein phosphatase 2C / Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / : / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 4-Layer Sandwich / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PYV / Protein phosphatase 2C 56 / Abscisic acid receptor PYL1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsZhou, X.E. / Melcher, K. / Ng, L.-M. / Soon, F.-F. / Xu, Y. / Suino-Powell, K.M. / Kovach, A. / Li, J. / Yong, E.-L. / Xu, H.E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Identification and mechanism of ABA receptor antagonism.
Authors: Melcher, K. / Xu, Y. / Ng, L.M. / Zhou, X.E. / Soon, F.F. / Chinnusamy, V. / Suino-Powell, K.M. / Kovach, A. / Tham, F.S. / Cutler, S.R. / Li, J. / Yong, E.L. / Zhu, J.K. / Xu, H.E.
History
DepositionJun 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Abscisic acid receptor PYL1
B: Protein phosphatase 2C 56
C: Abscisic acid receptor PYL1
D: Protein phosphatase 2C 56
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,25810
Polymers111,4064
Non-polymers8526
Water3,243180
1
A: Abscisic acid receptor PYL1
B: Protein phosphatase 2C 56
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1295
Polymers55,7032
Non-polymers4263
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-21 kcal/mol
Surface area19200 Å2
MethodPISA
2
C: Abscisic acid receptor PYL1
D: Protein phosphatase 2C 56
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1295
Polymers55,7032
Non-polymers4263
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-22 kcal/mol
Surface area19980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.978, 66.710, 72.598
Angle α, β, γ (deg.)115.78, 95.43, 105.60
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Abscisic acid receptor PYL1 / PYR1-like protein 1 / ABI1-binding protein 6 / Regulatory components of ABA receptor 9


Mass: 20534.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PYL1, RCAR12, At5g46790, MZA15.21 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8VZS8
#2: Protein Protein phosphatase 2C 56 / AtPP2C56 / Protein phosphatase 2C ABI1 / PP2C ABI1 / Protein ABSCISIC ACID-INSENSITIVE 1


Mass: 35168.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ABI1, At4g26080, F20B18.190 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P49597, protein-serine/threonine phosphatase
#3: Chemical ChemComp-PYV / 4-bromo-N-(pyridin-2-ylmethyl)naphthalene-1-sulfonamide / Pyrabactin


Mass: 377.256 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H13BrN2O2S / Comment: hormone*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.19 Å3/Da / Density % sol: 43.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2M ammonium sulphate, 0.1M BisTris, 22% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. all: 50236 / Num. obs: 46283 / % possible obs: 92 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.4 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 49.1

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0072refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3KDJ

3kdj


Resolution: 2.15→29.62 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / SU B: 15.115 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24751 3617 7.2 %RANDOM
Rwork0.2103 ---
obs0.21301 46283 96.99 %-
all-50236 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.935 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å2-1.47 Å2-2.38 Å2
2--0.11 Å21.22 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 2.15→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6956 0 48 180 7184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0227134
X-RAY DIFFRACTIONr_bond_other_d0.0030.024926
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.969649
X-RAY DIFFRACTIONr_angle_other_deg0.909311921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6775875
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.2823.253332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.062151228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2531568
X-RAY DIFFRACTIONr_chiral_restr0.0920.21076
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217905
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021487
X-RAY DIFFRACTIONr_mcbond_it1.8691.54405
X-RAY DIFFRACTIONr_mcbond_other0.7711.51782
X-RAY DIFFRACTIONr_mcangle_it3.30627114
X-RAY DIFFRACTIONr_scbond_it3.63832729
X-RAY DIFFRACTIONr_scangle_it5.4254.52535
X-RAY DIFFRACTIONr_rigid_bond_restr2.702312060
X-RAY DIFFRACTIONr_sphericity_free14.8775184
X-RAY DIFFRACTIONr_sphericity_bonded5.583511926
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 280 -
Rwork0.311 3118 -
obs--90.35 %

+
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