PDB-7z6e: Structure of the C1-PH-CNH regulatory module of MRCK1

ID or keywords:

Entry

Database: PDB / ID: 7z6e

Title

Structure of the C1-PH-CNH regulatory module of MRCK1

Components

Serine/threonine-protein kinase mrck-1

Keywords

LIPID BINDING PROTEIN / kinase / membrane / beta propeller / PH

Function / homology

Function and homology information

epithelial tube morphogenesis / RAC1 GTPase cycle / RHOQ GTPase cycle / nematode larval development / embryonic body morphogenesis / regulation of Golgi organization / positive regulation of endocytic recycling / embryonic morphogenesis / actomyosin structure organization / embryo development ending in birth or egg hatching ...
Similarity search - Function

Biological species

Caenorhabditis elegans (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.14 Å

Authors

Truebestein, L. / Leonard, T.A.

Funding support

Austria, 2items

Citation

Journal: Structure / Year: 2023
Title: Structure and regulation of the myotonic dystrophy kinase-related Cdc42-binding kinase.
Authors: Truebestein, L. / Antonioli, S. / Waltenberger, E. / Gehin, C. / Gavin, A.C. / Leonard, T.A.

History

Deposition	Mar 11, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 22, 2023	Provider: repository / Type: Initial release
Revision 1.1	Mar 22, 2023	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Apr 19, 2023	Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3	May 1, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	7z6e_validation.pdf.gz	5.1 MB	Display	wwPDB validaton report
Full document	7z6e_full_validation.pdf.gz	5.1 MB	Display
Data in XML	7z6e_validation.xml.gz	100.8 KB	Display
Data in CIF	7z6e_validation.cif.gz	143.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z6/7z6e ftp://data.pdbj.org/pub/pdb/validation_reports/z6/7z6e	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#195 - Mar 2016 RAF Protein Kinases similarity (5) #196 - Apr 2016 Lead Poisoning similarity (8) #152 - Aug 2012 cAMP-dependent Protein Kinase similarity (3) #222 - Jun 2018 Proteins and Nanoparticles similarity (5) #183 - Mar 2015 Phototropin similarity (3)

Deposited unit

A: Serine/threonine-protein kinase mrck-1

B: Serine/threonine-protein kinase mrck-1

C: Serine/threonine-protein kinase mrck-1

D: Serine/threonine-protein kinase mrck-1

E: Serine/threonine-protein kinase mrck-1

hetero molecules

327 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Serine/threonine-protein kinase mrck-1

hetero molecules

defined by author
65.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Serine/threonine-protein kinase mrck-1

hetero molecules

defined by author
65.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Serine/threonine-protein kinase mrck-1

hetero molecules

defined by author
65.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Serine/threonine-protein kinase mrck-1

hetero molecules

defined by author
65.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

E: Serine/threonine-protein kinase mrck-1

hetero molecules

defined by author
65.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	69.142, 97.467, 131.413
Angle α, β, γ (deg.)	81.380, 77.766, 80.394
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1
Symmetry operation	#1: x,y,z

#1: Protein	Serine/threonine-protein kinase mrck-1 / Myotonic dystrophy kinase-related CDC42-binding kinase homolog Mass: 65349.840 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: mrck-1, K08B12.5 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: O01583, non-specific serine/threonine protein kinase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1095 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.79 Å³/Da / Density % sol: 55.94 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 100 mM Bicine/Tris, pH 8.5 30 mM sodium nitrate 30 mM disodium hydrogen phosphate 30 mM ammonium sulfate 20% PEG550 MME 8% PEG20K 3% (v/v) glycerol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 21, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9762 Å / Relative weight: 1
Reflection	Resolution: 2.14→49.6 Å / Num. obs: 171288 / % possible obs: 94 % / Redundancy: 3.3 % / B_iso Wilson estimate: 35.63 Å² / CC_1/2: 0.993 / R_merge(I) obs: 0.122 / R_pim(I) all: 0.079 / Net I/σ(I): 6.92
Reflection shell	Resolution: 2.14→2.22 Å / Redundancy: 3.3 % / R_merge(I) obs: 1.167 / Mean I/σ(I) obs: 1.05 / Num. unique obs: 16283 / CC_1/2: 0.427 / R_pim(I) all: 0.7611 / % possible all: 89.6

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: AF-O01583-F1

Resolution: 2.14→49.6 Å / SU ML: 0.2931 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.8094
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2445	8479	4.98 %
R_work	0.1944	161670	-
obs	0.1969	170149	93.97 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 51.36 Å²

Refinement step

Cycle: LAST / Resolution: 2.14→49.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20716	0	10	1095	21821

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0078	21118
X-RAY DIFFRACTION	f_angle_d	0.941	28557
X-RAY DIFFRACTION	f_chiral_restr	0.0587	3248
X-RAY DIFFRACTION	f_plane_restr	0.0074	3651
X-RAY DIFFRACTION	f_dihedral_angle_d	6.6944	2828

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.14-2.16	0.3427	270	0.3195	4966	X-RAY DIFFRACTION	85.68
2.16-2.19	0.3312	247	0.3096	5146	X-RAY DIFFRACTION	90.64
2.19-2.22	0.3061	286	0.2907	5360	X-RAY DIFFRACTION	92.5
2.22-2.24	0.3403	285	0.2929	5309	X-RAY DIFFRACTION	93.3
2.24-2.27	0.3503	296	0.2962	5342	X-RAY DIFFRACTION	93.64
2.27-2.31	0.295	295	0.2827	5386	X-RAY DIFFRACTION	93.58
2.31-2.34	0.3245	316	0.2891	5313	X-RAY DIFFRACTION	93.68
2.34-2.37	0.3486	294	0.2781	5373	X-RAY DIFFRACTION	93.59
2.37-2.41	0.3471	252	0.2722	5293	X-RAY DIFFRACTION	92.62
2.41-2.45	0.3133	262	0.2587	5387	X-RAY DIFFRACTION	92.91
2.45-2.49	0.2757	267	0.2488	5127	X-RAY DIFFRACTION	89.91
2.49-2.54	0.2881	279	0.2383	5319	X-RAY DIFFRACTION	92.96
2.54-2.59	0.2689	271	0.2211	5477	X-RAY DIFFRACTION	94.9
2.59-2.64	0.2632	299	0.2286	5494	X-RAY DIFFRACTION	95.93
2.64-2.7	0.2747	285	0.2332	5432	X-RAY DIFFRACTION	95.05
2.7-2.76	0.2757	278	0.2346	5476	X-RAY DIFFRACTION	94.97
2.76-2.83	0.3095	286	0.2382	5412	X-RAY DIFFRACTION	94.86
2.83-2.9	0.2921	307	0.2285	5433	X-RAY DIFFRACTION	94.75
2.9-2.99	0.2458	251	0.2087	5442	X-RAY DIFFRACTION	93.68
2.99-3.09	0.2802	264	0.2076	5214	X-RAY DIFFRACTION	91.51
3.09-3.2	0.2593	294	0.1974	5504	X-RAY DIFFRACTION	96.15
3.2-3.32	0.2484	285	0.1961	5504	X-RAY DIFFRACTION	95.88
3.32-3.48	0.2545	319	0.1921	5498	X-RAY DIFFRACTION	96.12
3.48-3.66	0.2357	297	0.1752	5535	X-RAY DIFFRACTION	96.33
3.66-3.89	0.2164	286	0.1639	5465	X-RAY DIFFRACTION	95.28
3.89-4.19	0.1993	274	0.1537	5414	X-RAY DIFFRACTION	94.61
4.19-4.61	0.1718	273	0.1297	5620	X-RAY DIFFRACTION	97.29
4.61-5.28	0.1825	296	0.1384	5494	X-RAY DIFFRACTION	96.39
5.28-6.64	0.2208	284	0.1676	5415	X-RAY DIFFRACTION	94.59
6.64-49.6	0.1969	281	0.1612	5520	X-RAY DIFFRACTION	95.81

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	3.56426765598	1.11939173782	-1.14558559531	5.50330357067	-4.08616962032	6.92405721525	0.0399620226624	0.145927539891	-0.106985746808	0.163813424845	-0.0570380442133	-0.248331227471	-0.242864199305	0.32991271581	-0.0164214812176	0.173681380507	-0.00601189368944	-0.000534577259384	0.422311294766	-0.0697027356634	0.243566365399	25.9749946676	-3.21279335877	-31.88075765
2	4.08246407143	-0.26865912015	1.8257655586	0.50283577896	-0.0980473317455	1.44063399251	0.116428672557	-0.165286720671	-0.326097411076	0.0948232656179	0.00294268170798	-0.0194511024688	0.18003393008	-0.11380902523	-0.116156469534	0.356783439977	-0.0600704947552	0.0560278162184	0.297253817185	0.029388669549	0.200089412311	1.76343792439	-12.4453976675	-24.7825476349
3	1.64759672156	0.324906338619	-0.270710300114	1.60785793184	-0.3030489987	1.3652740171	-0.0941929988114	-0.00251155804244	0.0148087259737	-0.0597732724916	0.0358972563395	0.160376912597	0.0613859841532	-0.145505892388	0.0637224637412	0.22664114984	-0.0281038695795	0.00736792224966	0.379278997121	-0.0319764617681	0.142131061073	-16.0359194004	-0.36282795258	-48.9844734214
4	2.3077768389	-0.525844143357	0.813048757619	2.30526071622	-0.687165729619	1.38966890456	0.0592577912144	0.282031414603	0.108855553469	-0.0761298012212	-0.135015914	-0.0783410580002	0.0566857082129	0.246390319307	0.0453177933473	0.219319957659	-0.0371978537108	0.0332486042269	0.352989317309	-0.0265151230546	0.16270485143	3.56297195697	1.08380184848	-37.5909011729
5	2.60113287376	0.430842774702	1.51324536983	1.93592393265	1.85925106461	5.83805229402	0.0588960179069	-0.142244656797	-0.094645537614	0.0371047073236	-0.00759047179519	-0.108118390633	0.166762219832	0.354250713706	-0.069660911836	0.254553641318	0.0203450687688	0.0573913073088	0.424336562524	-0.0128796847336	0.243603508494	52.8448575348	8.73742836466	7.82190200877
6	1.55571779471	-0.600835062566	-0.435826083724	0.846770682994	0.396010285609	1.26466020847	-0.0182382323732	-0.0697592034962	-0.0348942059853	-0.038803484305	0.0318354630789	0.0635382850489	0.0280002357191	-0.132774621561	-0.0171831846383	0.265012705387	-0.041489444853	0.0265002710563	0.37767395381	0.0112906869752	0.177694492586	27.8743103201	15.5286560767	19.2795069538
7	5.4417854069	0.875602155825	0.880276985002	7.22729979716	0.743269706709	2.42091065365	0.2452874151	-0.615492425366	-0.573624779902	0.582256352706	-0.223013402602	-0.749552666202	0.141149394105	0.532945485575	-0.0787519639168	0.295044081803	0.046959119758	-0.025660825125	0.799681413303	0.0594327679829	0.42096974017	58.9166473869	-8.55561492613	60.4671100637
8	2.09187791414	-0.0174686284045	-1.04828687015	7.63205374036	0.578435025025	5.56975857137	0.177497322852	0.53295006507	-1.29469572102	-0.970215541038	-0.139579878158	-0.0417659696271	0.487820039461	0.159450056545	0.0265477867209	0.448771571634	0.185149134968	-0.146406021932	0.597101151995	-0.0985901315396	0.988090380963	49.0976586466	-27.3683206938	49.4453350238
9	5.62147761139	-2.0387183147	1.56489512548	2.8316053787	-0.676773654389	1.38273491411	0.352434664791	0.102119897903	-1.01665909099	-0.111773506546	-0.192946282567	-0.0909212786798	0.381396897055	0.0236059074692	-0.139193186437	0.365173403181	-0.0303182581275	-0.00612204093332	0.418251244223	-0.00874655628635	0.563017273087	25.4649250941	-19.9977164327	53.215471308
10	2.15030443265	0.616476768414	-0.280088439676	2.38963143087	-0.628624228564	0.920589302105	-0.0644863183791	0.0966535911628	-0.0626093869319	-0.063984590816	0.0646808144395	0.187802529658	-0.0515643073505	-0.274169389334	-0.00237910757232	0.249547494001	0.00820531865315	0.00855992796643	0.564329371822	-0.0377579983439	0.172173925254	14.0915789789	4.66618881506	50.0710738258
11	4.7200240283	-2.08664326426	-0.252090072698	3.94891464259	0.974707893082	2.15823121681	0.144274698766	0.0528544797634	0.458151826705	-0.182425382506	-0.0514019215121	-0.328267028959	-0.197472295374	0.0768710483999	-0.10337308878	0.244572232544	-0.0296878021151	0.0401563173932	0.447892218059	0.0304955677981	0.205603215078	36.1106296051	5.62041577809	56.8758950432
12	4.46730692969	2.24231332348	0.8599334177	6.4631027875	1.3314669321	5.06610055855	0.156759044659	-0.207967769007	-0.90146284292	0.0284022459266	-0.0170792789046	0.188262851281	0.29523625712	-0.198326522222	-0.111567548295	0.231127511913	0.0207328901011	-0.0476611014594	0.372845364103	0.0686146033123	0.413739476467	29.5707164937	-17.8844577088	57.7265829674
13	4.78615459575	-1.87215527417	0.597715178905	6.82223754216	-2.5345199258	5.07192771164	-0.0961503349199	-0.337183139574	0.00620105210235	-0.355414714456	-0.0726727573696	-0.531283822744	0.584097626505	0.68515725904	0.155518179096	0.261425908842	-0.0225639865355	-0.0156055417675	0.523157819415	0.0578855980839	0.528976092198	46.5648069164	-43.4224415938	17.8527589949
14	3.08399442209	0.608590279879	-0.473241661578	1.4077423478	-0.781656037365	1.60999382326	-0.0721465209402	-0.372727853732	0.472318348796	0.0795588201423	-0.0164663261861	0.0296980032894	-0.179192389673	-0.0158955233288	0.0702387512401	0.302622479805	0.0234590339373	-0.0937146665156	0.312656845542	-0.118097076318	0.346821450542	18.2487296955	-36.2657752512	18.5476272371
15	3.87815086214	-0.565945890257	-2.20036274619	1.93265703018	1.02341209937	7.77121447965	0.15555823359	0.326030816081	0.254227131761	-0.230219380229	0.0562104596936	-0.438798990042	-0.521509580157	0.306511508956	-0.189155299154	0.282775529427	-0.0653905859105	-0.0101338268058	0.522074197391	-0.0853090850444	0.514453111838	78.4172926114	-52.5779311727	-35.6682846579
16	5.16308816391	1.76335745415	1.76267009985	0.906470579614	0.845015017404	1.96615527991	0.108669437296	-0.315736346609	0.153597117824	0.190091525981	-0.18564744581	0.130324551963	0.0374577305688	-0.127904634266	0.0869123070902	0.432145984783	-0.00768277450047	-0.00543344500484	0.300094761216	-0.120460351223	0.472740544775	58.7109193817	-48.8774041242	-16.6510251785
17	5.2002906358	-2.34069265628	-1.95195633776	3.15986805772	1.86776983803	4.25333735695	-0.027223675917	-0.0391280731184	0.378039536336	0.143694049972	-0.0663059231337	0.366072435313	-0.0428354774479	-0.325803533902	0.0771512374941	0.234566623896	-0.037708513914	-0.0163399571009	0.240139978035	-0.0236417621981	0.359553737428	33.1874301953	-65.45841077	-38.0281053415
18	3.65759690445	0.606499588357	0.324710533861	2.57723188318	1.24885477686	5.53441605536	-0.0177406716191	0.196008688637	0.282181257106	-0.10038050087	0.0442235859694	0.0174604644405	-0.138160451929	0.147301925761	-0.0684251089537	0.223234850259	-0.0338419124616	-0.0267227948957	0.172051691046	0.0154652500217	0.325727714271	54.5392360815	-56.0200079041	-37.9029473368

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 957 through 1053 )	A	A	957 - 1053	1 - 89
2	2	chain 'A' and (resid 1054 through 1250 )	A	A	1054 - 1250	90 - 275
3	3	chain 'A' and (resid 1251 through 1331 )	A	A	1251 - 1331	276 - 356
4	4	chain 'A' and (resid 1332 through 1508 )	A	A	1332 - 1508	357 - 519
5	5	chain 'B' and (resid 957 through 1138 )	B	B	957 - 1138	1 - 174
6	6	chain 'B' and (resid 1139 through 1509 )	B	B	1139 - 1509	175 - 530
7	7	chain 'C' and (resid 957 through 1036 )	C	C	957 - 1036	1 - 80
8	8	chain 'C' and (resid 1037 through 1113 )	C	C	1037 - 1113	81 - 153
9	9	chain 'C' and (resid 1114 through 1250 )	C	C	1114 - 1250	154 - 285
10	10	chain 'C' and (resid 1251 through 1331 )	C	C	1251 - 1331	286 - 366
11	11	chain 'C' and (resid 1332 through 1438 )	C	C	1332 - 1438	367 - 463
12	12	chain 'C' and (resid 1439 through 1509 )	C	C	1439 - 1509	464 - 534
13	13	chain 'D' and (resid 957 through 1036 )	D	D	957 - 1036	1 - 76
14	14	chain 'D' and (resid 1037 through 1508 )	D	D	1037 - 1508	77 - 525
15	15	chain 'E' and (resid 957 through 1036 )	E	E	957 - 1036	1 - 74
16	16	chain 'E' and (resid 1037 through 1208 )	E	E	1037 - 1208	75 - 241
17	17	chain 'E' and (resid 1209 through 1331 )	E	E	1209 - 1331	242 - 361
18	18	chain 'E' and (resid 1332 through 1507 )	E	E	1332 - 1507	362 - 517

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