[English] 日本語
Yorodumi
- PDB-7p8c: Crystal structure of the Receiver domain of A. thaliana cytokinin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7p8c
TitleCrystal structure of the Receiver domain of A. thaliana cytokinin receptor AtCRE1 in complex with K+
ComponentsReceiver domain of histidine kinase 4
KeywordsSIGNALING PROTEIN / flavodoxin-like fold / cytokinin / phosphorelay
Function / homology
Function and homology information


cytokinin receptor activity / transmembrane histidine kinase cytokinin receptor activity / embryonic root morphogenesis / regulation of shoot system development / regulation of meristem development / carbohydrate homeostasis / : / cellular response to sucrose stimulus / regulation of seed germination / protein histidine kinase binding ...cytokinin receptor activity / transmembrane histidine kinase cytokinin receptor activity / embryonic root morphogenesis / regulation of shoot system development / regulation of meristem development / carbohydrate homeostasis / : / cellular response to sucrose stimulus / regulation of seed germination / protein histidine kinase binding / cytokinin-activated signaling pathway / protein histidine kinase activity / osmosensory signaling pathway / response to water deprivation / cellular response to phosphate starvation / myosin phosphatase activity / protein-serine/threonine phosphatase / histidine kinase / phosphorelay sensor kinase activity / phosphorelay signal transduction system / phosphoprotein phosphatase activity / defense response to bacterium / protein phosphorylation / endoplasmic reticulum membrane / protein kinase binding / enzyme binding / endoplasmic reticulum / plasma membrane
Similarity search - Function
CHASE domain superfamily / CHASE domain / CHASE domain profile. / CHASE / CHASE domain / : / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Phosphoribosyltransferase domain ...CHASE domain superfamily / CHASE domain / CHASE domain profile. / CHASE / CHASE domain / : / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Phosphoribosyltransferase domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
: / Histidine kinase 4
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsTran, L.H. / Urbanowicz, A. / Jasinski, M. / Jaskolski, M. / Ruszkowski, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreSONATA 2018/31/D/NZ1/03630 Poland
CitationJournal: Front Plant Sci / Year: 2021
Title: 3D Domain Swapping Dimerization of the Receiver Domain of Cytokinin Receptor CRE1 From Arabidopsis thaliana and Medicago truncatula .
Authors: Tran, L.H. / Urbanowicz, A. / Jasinski, M. / Jaskolski, M. / Ruszkowski, M.
History
DepositionJul 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Structure summary / Category: entity / Item: _entity.pdbx_description
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Receiver domain of histidine kinase 4
B: Receiver domain of histidine kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0294
Polymers29,9512
Non-polymers782
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-31 kcal/mol
Surface area15090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.319, 101.426, 33.549
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 916 through 1035 or resid 1118))
d_2ens_1chain "B"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASNPHEA1 - 120
d_21ens_1ASNPHEC1 - 120

-
Components

#1: Protein Receiver domain of histidine kinase 4 / Arabidopsis histidine kinase 4 / AtHK4 / Cytokinin receptor CYTOKININ RESPONSE 1 / AtCRE1 / ...Arabidopsis histidine kinase 4 / AtHK4 / Cytokinin receptor CYTOKININ RESPONSE 1 / AtCRE1 / Cytokinin receptor CRE1 / Phosphoprotein phosphatase AHK4 / Protein AUTHENTIC HIS-KINASE 4 / Protein ROOT AS IN WOL 1 / Protein WOODEN LEG


Mass: 14975.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AHK4, CRE1, RAW1, WOL, At2g01830, T23K3.2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9C5U0, histidine kinase, protein-serine/threonine phosphatase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.78 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES pH 7.0, 30% v/v Jeffamine M-600 pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→41.25 Å / Num. obs: 10946 / % possible obs: 62.2 % / Redundancy: 12.9 % / Biso Wilson estimate: 37.72 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.051 / Rrim(I) all: 0.184 / Net I/σ(I): 11.4
Reflection shellResolution: 2.15→2.39 Å / Redundancy: 11.5 % / Rmerge(I) obs: 1.23 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 544 / CC1/2: 0.73 / Rpim(I) all: 0.367 / Rrim(I) all: 1.286 / % possible all: 11.4

-
Processing

Software
NameVersionClassification
MxCuBEdata collection
STARANISOdata scaling
XDSdata reduction
PHENIX1.18.2_3874refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EUK

4euk


Resolution: 2.15→41.25 Å / SU ML: 0.3247 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.4287
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2842 554 5 %
Rwork0.2086 10517 -
obs0.2124 10946 64.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.71 Å2
Refinement stepCycle: LAST / Resolution: 2.15→41.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1968 0 2 41 2011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00882000
X-RAY DIFFRACTIONf_angle_d1.00912693
X-RAY DIFFRACTIONf_chiral_restr0.0549307
X-RAY DIFFRACTIONf_plane_restr0.0062345
X-RAY DIFFRACTIONf_dihedral_angle_d21.2211750
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.44789184932 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.380.346230.2742440X-RAY DIFFRACTION10.95
2.38-2.720.3239970.27231828X-RAY DIFFRACTION45.54
2.72-3.430.31182090.24073972X-RAY DIFFRACTION97.05
3.43-41.250.26382250.18474277X-RAY DIFFRACTION99.82
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)
14.453854178-5.590970608841.606783830117.02914533836-1.897661149382.44626917837-0.01197670231110.4083633016370.213153363725-1.00328533310.129934977365-1.081429435180.313360670376-0.169568878156-0.1313807957180.401790930582-0.07139154171310.07165505486830.389009377606-0.05534375989710.4756777448875.3232125603916.1412738971-1.6221284188
28.34751523034-0.190696654407-5.377353480364.271259507273.376966754655.969045108880.184352085434-0.974071678221-0.4984113575350.5471223203190.0218692806894-0.6733496198610.3301362407940.681812276481-0.2741771421650.5807510764170.0145026074482-0.05246828182470.2926038033670.1145687938380.3951105855949.7630211995822.25922444397.07025159698
33.83694323883-0.129454178145-3.105174970132.12078620894-2.163960592734.94305252141-0.477373846635-0.54548066421.48050877826-0.5653106141191.68043643292-0.62032671804-0.7817860132410.320247485623-0.5565208830890.527824992294-0.03735262507060.001610270153830.314602384868-0.1316244426290.60570438250910.977865266137.936911620919.1418771067
44.04751690424-1.340538030570.2118476699316.177217465861.588171474984.66361060056-0.136951984974-0.3583382587780.2297857639260.1621603952190.2382148152-0.21224634898-0.02586862498240.0944145481427-0.1322780084930.4747637657760.04488234660540.0389435051650.2611183205060.008542068930310.3314026401636.391481157223.03382864920.7325551848
53.09568450371-2.91370236718-2.312078946328.87796760714-2.264399582414.974328327440.4976032552450.4370360464960.8264771364470.6385336328860.4906821226532.62910415313-0.565218611787-1.99220712815-0.02980216789260.310278204436-0.1466982710880.1244982073960.3365057755630.004437323711390.375909507829-7.2789743170322.973861709716.8608696116
63.45144095488-0.979661723360.08188153249729.585322970870.2446417284832.26359676048-0.0841820471028-0.0402506440985-0.1630724115240.3305275710980.3621926792220.1799219970080.0771543808825-0.0931848392283-0.297623464350.26494099432-0.006286284135690.08302234554120.3118662319540.027252039210.257660252543-2.2598257403922.851107912613.4501804458
76.23782384601-4.47193063057-0.01819887971826.96370396804-0.2303561169054.28512880677-0.0164788732130.2601199462970.0510441205537-0.6143344133280.01901932140080.70188609140.0574227513408-1.024676589320.01617102835950.254382375360.0367420108406-0.01194057471330.4165348949010.02089862401920.369163841967-9.8886181707627.1369048215.81418502975
83.1544679416-3.456162556440.9731905383014.76476425467-0.5492212431554.30335190031-0.0225205427712-1.01993559780.488251143043-0.7377101971590.607910022269-0.0632720828166-0.425407412267-0.159836377894-0.2379852176460.3016235711570.07571050476510.006252103996820.2804771699030.02747584818210.345291154067-1.5627318165830.48580400057.55052645145
96.61106414844-1.54836451745-1.253956257448.798993063553.005703422688.510813479620.20251107675-0.2222115129570.6452609240680.454471350527-0.4674362515520.01712550847260.3285224050160.2483907103370.3487207463490.405285766532-0.02393340477490.02175497907920.3210649968210.0219854321890.33862199069513.38394000444.705424667077.53957465831
102.83176300913-0.6161063754392.898883933951.911120980880.9093711531844.36907150753-0.228262579256-0.2516299180420.695228941591-0.640185282578-0.4733889536210.212381774341-1.510435114030.04276575823930.5541839359810.3108723276910.125752876371-0.0395033414680.3268182691910.05996706226650.52543287460920.45449040287.00359917671-1.34682172132
114.925479094170.00169623359009-1.067515684346.87943239636-1.858362274344.736428603340.0948849685372-0.549634935765-0.498231654930.237104205354-0.170891788657-1.119163975460.6922469376130.7662988562650.1513208879320.4949601398440.0304028273370.01605913011910.439825631052-0.002773404449980.61784013145117.187836173222.8222825096-21.8619162342
128.132913560380.264748853313-1.173114475173.96234887864-1.775676194021.492068968130.154309545347-0.183655285484-0.7300666364470.149365669801-0.346658671483-0.231452647330.001842190086980.138376116050.2599147225790.335542724516-0.002265829694930.1069684128670.278030645361-0.03487176782730.27304021011625.72368009522.78096307022-11.9288856402
134.541076295090.1624425754570.03244004479962.07062648689-1.318080752993.05012151391-0.2358129685590.663240115435-0.352018686812-0.2923193158240.05682740544940.005463217420740.334898947205-0.07912875244010.1381323642850.307466414793-0.05941697059940.06921185745050.3176252548610.02698641152290.21894494874521.21229059725.28498186971-15.9980208588
146.38770978745-1.81362146838-0.4071715617666.845765351820.925001687475.075036481890.006293936386320.239938510804-0.462701329479-0.372181279702-0.1394876268240.1016508793180.0838794177164-0.006594646593880.1187138861130.28445456413-0.01261173461590.01746977905930.199907045061-0.00453454256750.19560064056717.1588795956-5.41969225819-8.91326134685
157.01315732216-4.755597789691.891667359498.926386853122.224240258163.46566488475-0.379498862432-0.924234404491-1.589671887080.04344434521880.3050011820470.7631510263520.740313082962-0.03650971946220.1188938440430.4478428825390.0393685226690.1564188181140.3421416401640.1084503272590.53599438061919.5175684688-13.0960915872-0.935804433393
168.61782139051-2.56417170912-0.9555669667480.912166327470.752618415951.49978683758-0.44301537468-1.727041097020.08438441411440.4805505451080.15596496155-1.350625963650.1863690933180.176886327715-0.08488292809860.4330833729650.1508279552410.1195462405560.3211211748950.05310282699370.39174129998128.847247101-11.7734387951-1.55733390233
173.67230500345-5.67281943383-0.7211986370069.020639326172.598126722947.26018644445-0.2061256191990.3131389205240.91588694963-0.1392958426960.698973380893-1.33681938277-1.16578420047-0.124652046934-0.1814102176840.1868675840810.05160948850690.1255851675630.2598846618310.05387868730990.30457038511118.7893529233.6471078322-2.94561729098
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 1012 through 1025 )BC1012 - 102597 - 110
22chain 'B' and (resid 1026 through 1035 )BC1026 - 1035111 - 120
33chain 'A' and (resid 916 through 922 )AA916 - 9221 - 7
44chain 'A' and (resid 923 through 953 )AA923 - 9538 - 38
55chain 'A' and (resid 954 through 961 )AA954 - 96139 - 46
66chain 'A' and (resid 962 through 980 )AA962 - 98047 - 65
77chain 'A' and (resid 981 through 999 )AA981 - 99966 - 84
88chain 'A' and (resid 1000 through 1011 )AA1000 - 101185 - 96
99chain 'A' and (resid 1012 through 1025 )AA1012 - 102597 - 110
1010chain 'A' and (resid 1026 through 1035 )AA1026 - 1035111 - 120
1111chain 'A' and (resid 1036 through 1048 )AA1036 - 1048121 - 133
1212chain 'B' and (resid 916 through 930 )BC916 - 9301 - 15
1313chain 'B' and (resid 931 through 953 )BC931 - 95316 - 38
1414chain 'B' and (resid 954 through 980 )BC954 - 98039 - 65
1515chain 'B' and (resid 981 through 999 )BC981 - 99966 - 84
1616chain 'B' and (resid 1000 through 1006 )BC1000 - 100685 - 91
1717chain 'B' and (resid 1007 through 1011 )BC1007 - 101192 - 96

+
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