PDB-6zzd: MB_CRS6-13 bound to CrSAS-6_N

ID or keywords:

Entry

Database: PDB / ID: 6zzd

Title

MB_CRS6-13 bound to CrSAS-6_N

Components

Centriole protein
MB_CRS6-13

Keywords

PROTEIN BINDING / Centriole / Cartwheel / Ring-polymer / Monobody

Function / homology

Spindle assembly abnormal protein 6, N-terminal / SAS-6, N-terminal domain superfamily / Centriolar protein SAS N-terminal domain / centriole / cell cycle / identical protein binding / cytoplasm / Centriole protein

Function and homology information

Biological species

Chlamydomonas reinhardtii (plant)

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Hatzopoulos, G.N. / Kukenshoner, T. / Banterle, N. / Favez, T. / Fluckiger, I. / Hantschel, O. / Gonczy, P.

Funding support

Switzerland, 2items

Citation

Journal: Nat Commun / Year: 2021
Title: Tuning SAS-6 architecture with monobodies impairs distinct steps of centriole assembly.
Authors: Hatzopoulos, G.N. / Kukenshoner, T. / Banterle, N. / Favez, T. / Fluckiger, I. / Hamel, V. / Andany, S. / Fantner, G.E. / Hantschel, O. / Gonczy, P.

History

Deposition	Aug 4, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 7, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6zzd.cif.gz	258.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6zzd.ent.gz	174.7 KB	Display	PDB format
PDBx/mmJSON format	6zzd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6zzd_validation.pdf.gz	334.9 KB	Display	wwPDB validaton report
Full document	6zzd_full_validation.pdf.gz	344.1 KB	Display
Data in XML	6zzd_validation.xml.gz	21.4 KB	Display
Data in CIF	6zzd_validation.cif.gz	29.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zz/6zzd ftp://data.pdbj.org/pub/pdb/validation_reports/zz/6zzd	HTTPS FTP

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Related structure data

Related structure data	6zz8C 6zzcC 6zzgC 3q0yS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2f1i-d 2fpk-d 2bbt-2 6jhw-1 4mvj-14 3roq-1 1t4g-d 3u4h-2 2fpl-d 3rok-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Deposited unit

A: Centriole protein

B: Centriole protein

C: MB_CRS6-13

D: MB_CRS6-13

64.2 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Centriole protein

D: MB_CRS6-13

defined by author
Evidence: isothermal titration calorimetry
32.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Centriole protein

C: MB_CRS6-13

defined by author
32.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	107.888, 65.722, 90.423
Angle α, β, γ (deg.)	90.000, 109.026, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
1	2
2	2

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	GLN	GLN	GLN	GLN	(chain 'A' and (resid 12 through 56 or resid 58 through 157))	A	A	12 - 55	14 - 57
1	2	1	ASN	ASN	PRO	PRO	(chain 'A' and (resid 12 through 56 or resid 58 through 157))	A	A	58 - 156	60 - 158
2	3	1	GLN	GLN	GLN	GLN	(chain 'B' and (resid 12 through 56 or resid 58 through 157))	B	B	12 - 55	14 - 57
2	4	1	ASN	ASN	PRO	PRO	(chain 'B' and (resid 12 through 56 or resid 58 through 157))	B	B	58 - 156	60 - 158
1	5	2	GLN	GLN	THR	THR	(chain 'C' and resid -2 through 93)	C	C	-2 - 93	31 - 126
2	6	2	GLN	GLN	THR	THR	chain 'D'	D	D	-2 - 93	31 - 126

NCS ensembles :

ID
1
2

#1: Protein	Centriole protein Mass: 18016.543 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CrSAS-6, CHLRE_12g516950v5 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A9CQL4
#2: Protein	MB_CRS6-13 Mass: 14078.626 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.36 Å³/Da / Density % sol: 47.9 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 15% PEG 4000, 0.2M magnesium chloride hexahydrate, 0.1 M Tris pH 8.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.05→43.06 Å / Num. obs: 255461 / % possible obs: 98.7 % / Redundancy: 6.9 % / B_iso Wilson estimate: 45.87 Å² / R_merge(I) obs: 0.086 / Net I/σ(I): 13.03
Reflection shell	Resolution: 2.051→2.125 Å / R_merge(I) obs: 1.451 / Num. unique obs: 3640

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Processing

Software

Name	Version	Classification
PHENIX	1.15_3459	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3q0y

3q0y

Resolution: 2.05→43.06 Å / SU ML: 0.3142 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.8779
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2281	3622	5 %
R_work	0.1986	68755	-
obs	0.2002	72377	98.39 %

Solvent computation

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

Displacement parameters

B_iso mean: 72.41 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→43.06 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3877	0	0	155	4032

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0095	3981
X-RAY DIFFRACTION	f_angle_d	1.1713	5426
X-RAY DIFFRACTION	f_chiral_restr	0.1297	626
X-RAY DIFFRACTION	f_plane_restr	0.0083	696
X-RAY DIFFRACTION	f_dihedral_angle_d	11.8261	2647

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 (%)
2.05-2.08	0.4651	129	0.4064	2477	X-RAY DIFFRACTION	93.64
2.08-2.11	0.3668	143	0.3637	2716	X-RAY DIFFRACTION	96.69
2.11-2.14	0.3448	129	0.3473	2494	X-RAY DIFFRACTION	97.26
2.14-2.17	0.3662	140	0.3553	2633	X-RAY DIFFRACTION	96.96
2.17-2.2	0.3583	140	0.3195	2641	X-RAY DIFFRACTION	97.24
2.2-2.24	0.3763	138	0.3201	2602	X-RAY DIFFRACTION	97.82
2.24-2.28	0.3465	142	0.3069	2660	X-RAY DIFFRACTION	98.28
2.28-2.32	0.2965	137	0.2792	2613	X-RAY DIFFRACTION	98.35
2.32-2.36	0.2878	141	0.2725	2666	X-RAY DIFFRACTION	98.46
2.36-2.41	0.3279	137	0.2735	2654	X-RAY DIFFRACTION	98.52
2.41-2.46	0.3248	139	0.2741	2627	X-RAY DIFFRACTION	98.54
2.46-2.52	0.3315	137	0.2612	2666	X-RAY DIFFRACTION	98.42
2.52-2.58	0.3272	139	0.2514	2630	X-RAY DIFFRACTION	98.75
2.58-2.65	0.2974	145	0.2438	2715	X-RAY DIFFRACTION	99.03
2.65-2.73	0.2664	140	0.232	2639	X-RAY DIFFRACTION	98.79
2.73-2.82	0.2815	141	0.2241	2634	X-RAY DIFFRACTION	99
2.82-2.92	0.2454	140	0.2169	2640	X-RAY DIFFRACTION	99.14
2.92-3.04	0.267	142	0.2211	2695	X-RAY DIFFRACTION	99.09
3.04-3.18	0.271	143	0.2138	2676	X-RAY DIFFRACTION	99.37
3.18-3.34	0.25	138	0.1889	2649	X-RAY DIFFRACTION	99.18
3.34-3.55	0.1961	140	0.1933	2663	X-RAY DIFFRACTION	99.4
3.55-3.83	0.1928	137	0.1758	2671	X-RAY DIFFRACTION	99.15
3.83-4.21	0.1842	141	0.166	2675	X-RAY DIFFRACTION	99.58
4.21-4.82	0.1451	144	0.1329	2681	X-RAY DIFFRACTION	99.33
4.82-6.07	0.1646	141	0.1447	2665	X-RAY DIFFRACTION	99.26
6.07-43.06	0.203	139	0.1694	2673	X-RAY DIFFRACTION	99.08

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	6.02531011837	1.66424666069	-0.84372814766	5.24691536714	-0.529911785465	7.40532800731	-0.1669538228	-0.0854925527177	0.482178499564	-0.110301885595	0.090756979738	0.384179863251	-0.346752234579	-0.66771404725	0.106104353341	0.281508169299	0.148690910518	-0.0553005935103	0.631761590457	-0.0486862251493	0.442629446688	23.1466628904	6.32818760903	25.341254244
2	1.44712257322	-0.77281981765	0.298180211218	2.59926047611	1.11482943119	6.04260338018	0.496519887349	-0.537924748275	0.880560386725	0.68646855675	0.135004174601	0.741674439021	-0.371898249605	-1.02484229385	-0.255832057347	0.55221357051	0.0808850919088	0.270331103887	0.82204024135	-0.145683982726	0.6372594202	19.2785566515	7.43927572517	33.9589307545
3	5.0676608469	-0.273443352937	-3.36702975591	4.42936576855	1.58193996035	6.27581395028	0.0911454526937	0.818797222574	0.617291239226	-0.125414004636	0.119804461111	0.846988357312	-0.341157631222	-1.16132305863	-0.330432896184	0.43438565896	0.157476088079	-0.0142515331218	0.66215854715	0.0273610391361	0.559624888264	23.4273179814	10.4449028979	21.1953045751
4	6.70169642406	-0.437287602068	-4.11331056372	9.29424952916	0.779910002909	8.99572298594	0.0352722152528	-0.77723809778	1.57346169771	-0.0177422004965	0.232838227771	-0.804115808827	-0.729908954302	0.685622213415	-0.215460100376	0.492603443335	0.0282512248007	-0.0204263746039	0.504712259856	-0.145835839517	0.545613576323	34.6983339319	12.9945781987	25.93239221
5	6.13941365795	0.404350904491	-1.1116236917	3.2108799012	0.917195836722	6.60280173507	0.159230188736	-1.34401237406	-0.240092457783	0.457435193031	-0.161098407354	0.204543334895	-0.0479700733093	0.0164089698927	-0.032528202776	0.383834464477	0.0350654081412	-0.0577044592	0.683674778576	-0.0135998537169	0.318471216163	30.9586203522	1.11539006947	35.4113239478
6	9.30178292646	1.65850533921	3.98366460671	1.89098523511	-0.792614611815	6.35613915235	0.204408074006	-0.974792351662	-0.0595239566653	0.0866650422888	-0.0137384674023	-0.0110069447566	0.359593077918	-0.834830399764	-0.179247606363	0.47394011863	0.0175723021195	0.0511879839557	0.843194207024	-0.165632968515	0.315846510733	30.7405086079	6.55416855046	42.6070506468
7	8.38089612808	-0.422648539649	-1.12275425574	6.89723678976	-2.37710728447	4.68733348514	0.507566511768	0.069104332965	0.730560214983	0.649003968874	-0.609387877751	-0.0099595270176	-0.694052456428	0.893545670504	0.0832460041254	0.562093786046	-0.0235976676251	0.0709003829049	0.601676569856	-0.1819052916	0.523295262169	29.9969120688	10.1958602703	35.5085399329
8	5.78074058287	0.740427260752	-0.406778278895	3.39734472486	-0.257469403935	4.05800409751	-0.2029027304	0.246237779425	-0.716126863571	-0.0305999245178	0.0375146059258	-0.115397535449	0.487757926688	0.251118344384	0.0916632041434	0.38133349711	0.0620400679244	0.0339661873828	0.258531131325	-0.00900019911172	0.3389017937	-3.03597694462	15.0440177612	13.3183984312
9	8.07083039308	1.67215210248	-0.506541397118	4.39068461799	-0.0930257895661	3.76636106701	-0.0351556155259	-0.67229895917	-0.654670173957	0.280537436295	0.00500527501729	0.00242032225504	0.354640300291	0.112448487485	0.0223255814564	0.336242567338	0.0935850699028	-0.0176300153355	0.396371876051	0.138606983335	0.344296306372	-8.15255522863	16.0836857087	20.9162112831
10	6.28645740311	-1.71548092159	-3.71841454582	7.37738702354	0.333134928489	8.62642944443	-0.0829663822762	-0.555289312451	-0.275484219716	0.785601515842	0.181161136343	-0.48391822549	0.151068718589	0.22926528228	-0.189703796082	0.348187266602	0.110380583424	-0.0976450746212	0.610187099837	0.0864177904018	0.397376441737	3.80856247972	18.1573160031	24.1246521105
11	2.672636004	-3.42792682532	3.27903796765	4.79186404952	-4.75987737134	4.80621240737	-0.623909580223	-0.16854595708	3.34322566533	-0.00300922210603	0.276937733245	-0.56092919509	-2.28247744353	-2.75523716147	-0.13298908562	1.19898467758	0.281162149121	-0.142792950337	1.05936290358	0.0364958087874	1.52448120619	7.70822879129	47.0170906694	-14.0537453704
12	2.40846667512	-0.226943936513	0.935245654051	2.7539426004	-1.09524223511	7.66497256197	-0.0423434635211	-0.499155000915	-0.0819358366444	0.269667457095	-0.0653405198349	-0.430555111818	-0.21962562252	0.671570671408	0.109405811193	0.309366254413	-0.0545008238429	-0.0233340852191	0.523126383041	0.00677289598894	0.352036645409	16.0112443825	28.1666394343	3.00855187879
13	0.47124821692	-0.422993157907	-0.054049376119	1.49978879268	-0.235752353137	1.57407500955	0.312960752449	-0.288885476429	0.125805599554	0.456260223516	-0.21917355735	-0.371941657995	-0.131730092683	0.997785084936	-0.0638294556812	0.482087043605	-0.15921381677	-0.0606122378138	0.57151807625	-0.0258184949129	0.396094473562	18.5329207554	33.1863881827	-5.0087683475
14	7.06334565166	-0.211693150482	1.14691359732	4.71243359202	0.899696824402	4.32015342474	-0.114496592559	0.216572333726	-1.13363073497	-0.395113434097	-0.0776579506749	0.929678144179	0.285683694171	-0.838416988091	0.119059483696	0.408841212702	-0.121965231628	0.0607434427475	0.719379095729	-0.0394355444396	0.735276417939	14.517243613	-15.5210573615	22.2656964998
15	3.82523554351	2.74004442997	4.98869081278	6.61011361584	3.78783094756	6.5314683262	-0.322238686744	1.40052447864	-0.905099390191	-1.23025667877	0.338367288179	0.62180152547	-0.364680857274	-1.31183513319	-0.0273469713804	0.482120350827	-0.112508228127	-0.0922532004791	1.32380814142	-0.138939012403	0.591621598027	16.0566132261	-9.85482803731	13.5056606863
16	0.570162562334	1.4513368086	-0.389221920396	4.50611085438	-1.73313164532	0.959847279543	0.354788074911	-0.12900451031	0.208703081046	-2.56707259691	-0.812946567652	0.0386925027071	-0.37960795502	-0.12011826081	0.523080167456	1.56152038249	-0.453714223751	0.226542250119	2.16890290471	-0.484153429854	1.03704655308	15.9199582197	-14.0318361598	0.620796837994
17	3.1638866517	3.45580796894	3.54913061814	3.89597037047	3.91186181066	3.98328185073	-0.849111492437	2.25440203211	-0.242031309361	-1.57121445325	-0.118142714302	-0.342631239122	-0.981144622989	0.471114318297	1.17564021724	0.72852998929	0.00377722816783	-0.0582338361241	1.22807471375	-0.0199249024247	0.542701351216	16.0855498047	-5.08830634524	14.9689613699
18	3.41546064386	-0.668010522204	2.20960558843	0.717214532366	0.56237610339	3.00982512036	-0.35481117359	0.398438846212	0.218773653247	-0.64184840966	0.113602160483	2.10871091237	0.785437194833	-0.693476296079	0.821563918293	0.83366105854	-0.371738266421	-0.419224626759	1.30392887685	-0.108759335594	1.14631042099	7.45237954776	-10.0240890625	14.086661272
19	2.58452171461	-0.0129406339662	2.04025652015	5.9237998025	-1.02354911383	5.52876092139	-0.13299152451	0.0542985110588	-0.368471741911	-0.416074077099	-0.27287917862	0.324070720894	0.23216969126	-0.978908278008	0.251190743262	0.437312781766	-0.0512601768618	0.0383511318824	0.646158768189	-0.0824532868836	0.480673959289	24.5525115715	-13.3074536585	17.4133092762
20	1.99949337153	-2.58871205996	6.31431941327	5.9087360562	-3.58699176298	6.16985838802	0.315775779288	0.741226414221	-0.989910650116	-2.24123843646	0.243244671764	1.9315314827	0.942064375271	-1.56633740773	0.0823406294698	0.917705761516	-0.314448630204	-0.326243396044	1.08036531834	-0.386658966595	1.64974563699	8.8066250157	-19.6838083777	11.1425216739

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 11 through 34 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 35 through 52 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 53 through 74 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 75 through 91 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 92 through 130 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 131 through 145 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 146 through 157 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 12 through 52 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 53 through 121 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 122 through 158 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid -8 through 1 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 2 through 75 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 76 through 93 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid -2 through 30 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 31 through 38 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 39 through 45 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 46 through 51 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 52 through 66 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 67 through 86 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 87 through 93 )

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