[English] 日本語
Yorodumi
- PDB-3rt0: Crystal structure of PYL10-HAB1 complex in the absence of abscisi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rt0
TitleCrystal structure of PYL10-HAB1 complex in the absence of abscisic acid (ABA)
Components
  • Abscisic acid receptor PYL10
  • Protein phosphatase 2C 16
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PYL10-HAB1 binary COMPLEX / apo-PYL10 inhibits HAB1 dephosphorylation activity / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / protein-serine/threonine phosphatase / protein serine/threonine phosphatase activity / signaling receptor activity / protein homodimerization activity / metal ion binding / nucleus / 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
Abscisic acid receptor PYL10 / Protein phosphatase 2C 16
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.113 Å
AuthorsHao, Q. / Yin, P. / Li, W. / Wang, L. / Yan, C. / Wang, J. / Yan, N.
CitationJournal: Mol.Cell / Year: 2011
Title: The Molecular Basis of ABA-Independent Inhibition of PP2Cs by a Subclass of PYL Proteins
Authors: Hao, Q. / Yin, P. / Li, W. / Wang, L. / Yan, C. / Lin, Z. / Wu, J.Z. / Wang, J. / Yan, S.F. / Yan, N.
History
DepositionMay 2, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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: Protein phosphatase 2C 16
B: Protein phosphatase 2C 16
C: Abscisic acid receptor PYL10
D: Abscisic acid receptor PYL10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,8726
Polymers116,8244
Non-polymers492
Water9,134507
1
A: Protein phosphatase 2C 16
C: Abscisic acid receptor PYL10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4363
Polymers58,4122
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-10 kcal/mol
Surface area23790 Å2
MethodPISA
2
B: Protein phosphatase 2C 16
D: Abscisic acid receptor PYL10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4363
Polymers58,4122
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-11 kcal/mol
Surface area22240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.766, 83.503, 88.544
Angle α, β, γ (deg.)90.00, 97.20, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Protein phosphatase 2C 16 / AtPP2C16 / AtP2C-HA / Protein HYPERSENSITIVE TO ABA 1 / Protein phosphatase 2C HAB1 / PP2C HAB1


Mass: 37753.219 Da / Num. of mol.: 2 / Fragment: residues 172- 511 / Mutation: C274S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HAB1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9CAJ0, protein-serine/threonine phosphatase
#2: Protein Abscisic acid receptor PYL10 / ABI1-binding protein 8 / PYR1-like protein 10 / Regulatory components of ABA receptor 4


Mass: 20658.545 Da / Num. of mol.: 2 / Mutation: C166S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PYL10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8H1R0
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 507 / 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: 2.22 Å3/Da / Density % sol: 44.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100mM Tris, 21% PEG3350, 2% Dioxane , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 27, 2010
RadiationMonochromator: rotated-inclined double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→35 Å / Num. obs: 58037 / % possible obs: 99.8 % / Biso Wilson estimate: 25.43 Å2
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 4.16 / Num. unique all: 5772 / Rsym value: 0.399 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
BSSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.3_473)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RT2

3rt2


Resolution: 2.113→32.499 Å / Occupancy max: 1 / Occupancy min: 0.12 / FOM work R set: 0.8629 / SU ML: 0.24 / σ(F): 0 / Phase error: 21.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2067 2848 5.1 %
Rwork0.173 --
obs0.1748 55874 95.24 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.02 Å2 / ksol: 0.338 e/Å3
Displacement parametersBiso max: 203.27 Å2 / Biso mean: 36.291 Å2 / Biso min: 9.77 Å2
Baniso -1Baniso -2Baniso -3
1--1.8226 Å2-0 Å25.357 Å2
2---3.7385 Å2-0 Å2
3---5.5611 Å2
Refinement stepCycle: LAST / Resolution: 2.113→32.499 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7592 0 2 507 8101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.027881
X-RAY DIFFRACTIONf_angle_d1.07410657
X-RAY DIFFRACTIONf_chiral_restr0.0711200
X-RAY DIFFRACTIONf_plane_restr0.0051382
X-RAY DIFFRACTIONf_dihedral_angle_d17.1212964
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1135-2.14990.2992780.21322090216874
2.1499-2.1890.24981420.20012431257389
2.189-2.23110.28651500.19952484263490
2.2311-2.27660.22081190.18332601272093
2.2766-2.32610.23381290.17962599272893
2.3261-2.38020.21881200.17912628274894
2.3802-2.43970.22461400.18762601274194
2.4397-2.50570.22061590.18992609276895
2.5057-2.57940.25461660.18912602276895
2.5794-2.66260.28261450.18582722286797
2.6626-2.75770.2241340.18222724285897
2.7577-2.86810.20641350.18442738287398
2.8681-2.99850.21921570.18342700285799
2.9985-3.15650.24071490.18432757290699
3.1565-3.3540.20721690.17652756292599
3.354-3.61270.18681460.169827852931100
3.6127-3.97570.15451590.154727792938100
3.9757-4.54960.18721400.143927952935100
4.5496-5.72690.17671580.147428042962100
5.7269-32.50310.18391530.18252821297498
Refinement TLS params.Method: refined / Origin x: 37.9109 Å / Origin y: 15.0621 Å / Origin z: 12.3016 Å
111213212223313233
T0.1137 Å2-0.0009 Å2-0.0106 Å2-0.0984 Å20.0132 Å2--0.1202 Å2
L0.3087 °2-0.0568 °2-0.1667 °2-0.1811 °20.1248 °2--0.1284 °2
S0.019 Å °-0.0173 Å °-0.0316 Å °0.0023 Å °0.0057 Å °-0.04 Å °-0.0187 Å °0.0088 Å °-0.0197 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA180 - 510
2X-RAY DIFFRACTION1allB180 - 506
3X-RAY DIFFRACTION1allC13 - 184
4X-RAY DIFFRACTION1allD19 - 184
5X-RAY DIFFRACTION1allA - C1 - 507
6X-RAY DIFFRACTION1allA - B1 - 512

+
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