PDB-7a9b: Crystal structure of Shank1 PDZ domain with ARAP3-derived peptide

ID or keywords:

Entry

Database: PDB / ID: 7a9b

Title

Crystal structure of Shank1 PDZ domain with ARAP3-derived peptide

Components

SH3 and multiple ankyrin repeat domains protein 1,Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3

Keywords

PROTEIN BINDING / Shank1 / PDZ domain / protein-protein interaction / internal peptide binding motif / ARAP3 / Structural Genomics / Structural Genomics Consortium / SGC

Function / homology

Function and homology information

somatostatin receptor binding / determination of affect / synaptic receptor adaptor activity / synapse maturation / olfactory behavior / Neurexins and neuroligins / negative regulation of actin filament bundle assembly / structural constituent of postsynaptic density / righting reflex / protein localization to synapse ...
Similarity search - Function

Biological species

Rattus norvegicus (Norway rat)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Mariam McAuley, M. / Ali, M. / Ivarsson, Y. / Knapp, S. / Joerger, A.C. / Structural Genomics Consortium (SGC)

Funding support

1items

Citation

Journal: to be published
Title: Crystal structure of Shank1 PDZ domain with ARAP3-derived peptide
Authors: Mariam McAuley, M. / Ali, M. / Ivarsson, Y. / Knapp, S. / Joerger, A.C. / Structural Genomics Consortium (SGC)

History

Deposition	Sep 1, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 21, 2020	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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7a9b.cif.gz	135.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7a9b.ent.gz	87.8 KB	Display	PDB format
PDBx/mmJSON format	7a9b.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7a9b_validation.pdf.gz	444.9 KB	Display	wwPDB validaton report
Full document	7a9b_full_validation.pdf.gz	446.9 KB	Display
Data in XML	7a9b_validation.xml.gz	12.5 KB	Display
Data in CIF	7a9b_validation.cif.gz	17.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a9/7a9b ftp://data.pdbj.org/pub/pdb/validation_reports/a9/7a9b	HTTPS FTP

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Related structure data

Related structure data	1q3oS S: Starting model for refinement
Similar structure data	5fws-d 2gs4-d 2pu9-2 5fwt-d 6cey-4 5y87-2 4iua-8 5iqb-1 3plf-2 6c5u-2 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
Related items in Molecule of the Month	#148 - Apr 2012 Ras Protein similarity (3) #35 - Nov 2002 Ferritin and Transferrin similarity (4) #245 - May 2020 Spliceosomes similarity (1)

Deposited unit

A: SH3 and multiple ankyrin repeat domains protein 1,Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3

B: SH3 and multiple ankyrin repeat domains protein 1,Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	67.799, 67.799, 248.967
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	178
Space group name H-M	P6₁22
Space group name Hall	P6₁2(x,y,z+5/12)
Symmetry operation	#1: x,y,z #2: x-y,x,z+1/6 #3: y,-x+y,z+5/6 #4: -y,x-y,z+1/3 #5: -x+y,-x,z+2/3 #6: x-y,-y,-z #7: -x,-x+y,-z+2/3 #8: -x,-y,z+1/2 #9: y,x,-z+1/3 #10: -y,-x,-z+5/6 #11: -x+y,y,-z+1/2 #12: x,x-y,-z+1/6

#1: Protein	SH3 and multiple ankyrin repeat domains protein 1,Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3 / Shank1 / GKAP/SAPAP-interacting protein / SPANK-1 / Somatostatin receptor-interacting protein / ...Shank1 / GKAP/SAPAP-interacting protein / SPANK-1 / Somatostatin receptor-interacting protein / SSTRIP / Synamon / Centaurin-delta-3 / Cnt-d3 Mass: 15061.116 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Homo sapiens (human) Gene: Shank1, ARAP3, CENTD3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WV48, UniProt: Q8WWN8
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.01 Å³/Da / Density % sol: 59.14 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 nL of protein solution (15 mg/ml mutant protein in 10 mM HEPES buffer, pH 8.0, 150 mM NaCl, 5% (v/v) glycerol and 0.5 mM TCEP) were mixed with 100 nL reservoir buffer (16% (w/v) ...Details: 100 nL of protein solution (15 mg/ml mutant protein in 10 mM HEPES buffer, pH 8.0, 150 mM NaCl, 5% (v/v) glycerol and 0.5 mM TCEP) were mixed with 100 nL reservoir buffer (16% (w/v) polyethylene glycol 3350 and 0.2 M ammonium citrate), above a reservoir volume of 20 microL

Crystal

Density Matthews: 3.01 Å³/Da / Density % sol: 59.14 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 nL of protein solution (15 mg/ml mutant protein in 10 mM HEPES buffer, pH 8.0, 150 mM NaCl, 5% (v/v) glycerol and 0.5 mM TCEP) were mixed with 100 nL reservoir buffer (16% (w/v) ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 1, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.999 Å / Relative weight: 1
Reflection	Resolution: 2→47.932 Å / Num. obs: 24047 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 9.2 % / B_iso Wilson estimate: 31.7924470837 Å² / CC_1/2: 0.999 / Net I/σ(I): 12.2
Reflection shell	Resolution: 2→2.05 Å / Redundancy: 9.5 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1716 / CC_1/2: 0.78 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
PHENIX	1.10.1_2155	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1Q3O

1q3o

Resolution: 2→47.9319903751 Å / SU ML: 0.242939563759 / Cross valid method: FREE R-VALUE / σ(F): 1.34056753806 / Phase error: 24.0847388415
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.249057148164	1209	5.0492816572 %
R_work	0.200578430683	22735	-
obs	0.203122312625	23944	99.887363898 %

Solvent computation

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

Displacement parameters

B_iso mean: 44.1341826172 Å²

Refinement step

Cycle: LAST / Resolution: 2→47.9319903751 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1858	0	4	122	1984

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.00609183812312	1902
X-RAY DIFFRACTION	f_angle_d	0.760141956248	2574
X-RAY DIFFRACTION	f_chiral_restr	0.0496298246419	297
X-RAY DIFFRACTION	f_plane_restr	0.00612171623386	335
X-RAY DIFFRACTION	f_dihedral_angle_d	16.6665662376	1126

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 (%)
2-2.0801	0.270098242722	123	0.23587421838	2425	X-RAY DIFFRACTION	99.5701445877
2.0801-2.1748	0.275154006156	121	0.225367939742	2491	X-RAY DIFFRACTION	99.8852772467
2.1748-2.2894	0.247891903931	122	0.220964076442	2452	X-RAY DIFFRACTION	99.8835855646
2.2894-2.4329	0.27163463934	137	0.226625580007	2488	X-RAY DIFFRACTION	100
2.4329-2.6207	0.268503219088	123	0.225817128744	2494	X-RAY DIFFRACTION	99.8854961832
2.6207-2.8844	0.282398960233	136	0.222633845319	2496	X-RAY DIFFRACTION	100
2.8844-3.3017	0.276736808238	138	0.211168226496	2540	X-RAY DIFFRACTION	99.962672639
3.3017-4.1594	0.261191599714	158	0.169459852261	2567	X-RAY DIFFRACTION	100
4.1594-47.9	0.202105476269	151	0.188044488425	2782	X-RAY DIFFRACTION	99.8638066054

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	6.00683081938	2.96170956847	4.9505436875	5.53206932105	2.64804579478	4.08780677702	-0.0163101107993	0.123848769991	-0.39817463603	0.0840013911058	-0.758615463675	-0.0338566688533	0.258554926292	-0.601893048666	0.661763553718	0.589083563658	-0.185109280725	0.127671231937	0.856302488965	0.0231071399424	0.903403077535	-15.6654543131	-3.88434434456	-18.7561123862
2	3.71120141531	4.55388065473	-3.07649161238	5.60295410867	-3.76847349987	2.58695139513	-0.0893662860762	-0.254835550278	0.0335489537129	-0.571541741204	-0.166628012219	0.142575887768	-0.509735681886	0.0361217548327	0.099414194224	0.528637578636	-0.156043359896	-0.0360680722376	0.193348197586	0.0120631252277	0.376289517711	1.57472165015	13.3397291104	-21.7698352851
3	1.67487469454	1.06271357098	-0.988099411738	2.96477922107	-0.965154547411	1.39606527099	-0.070434182053	0.0145468494464	0.195184581437	-0.272055523438	0.214226836738	-0.327667420036	-0.613230241617	0.605610985923	0.108098638336	0.622939802163	-0.564521075565	0.0182918943935	0.131078449811	0.0110642084313	0.369833911513	13.0700883167	21.4304097146	-12.9048451988
4	8.19513309558	-1.18262902349	-3.07157209695	7.61627887656	1.04314076673	3.03464284888	0.262988554792	-0.919985607171	-2.89754962773	1.25589387105	-0.36742626558	-1.67835676279	1.51446934274	1.02020989884	-0.0381908788294	0.583277155537	-0.000108157711874	-0.107566652094	0.544674019723	0.144589446691	1.03400537955	14.866417099	-3.03367809793	-9.48000049106
5	4.81491100614	0.420986664915	0.309765569313	3.35403647066	-1.28757880304	4.00612618418	0.0923709244719	-0.0475523746628	-0.553503284811	0.0695802130247	-0.0848374388157	0.0979767503656	0.207709093165	0.161933704784	0.020358462259	0.245656002719	-0.070787005621	-0.000855291245952	0.17699681187	0.0173487349758	0.291418234348	5.09978996095	5.17984217667	-12.9689615018
6	2.59358647215	0.263380987808	-0.336566414296	8.09739570276	-1.35607360712	1.69781497313	0.218078842035	-0.068605286587	0.418822920057	0.413189956139	0.109955510173	0.314800633931	-0.492475159137	-0.034148328024	0.0118824833524	0.91456259068	-0.245893908457	0.0742067078786	0.0202048812458	0.0347375258549	0.331417339616	4.1167062427	25.2901957465	-13.8548479276
7	3.26968589022	-1.75103406439	-2.00802485316	3.45148168739	0.943322381927	2.56956442815	0.169903596199	0.125279782653	0.0446219019371	-0.236912492871	-0.114979963332	0.0345989504817	-0.487244783337	0.0301408114895	-0.0223825095411	0.377946719255	-0.118768412489	-0.0300760335827	0.228725084009	0.041382983034	0.320108678087	4.57170022654	12.8956353983	-16.4987200815
8	3.07950469085	-1.9083426567	2.63629582124	2.10179952068	-2.95580985328	4.29836398629	-0.0613906301737	0.487266427459	-0.108660387741	-0.396007327412	-0.273986914369	-0.63256398419	-0.390033981749	1.0109917712	0.352410703048	0.309228760919	-0.127404154516	0.0342213799063	0.323347410229	0.0332526526797	0.345168099917	13.5528541693	6.1673645305	-20.8148182755
9	4.13484410245	1.99060169317	-2.27950238891	1.86576679785	-2.12675661338	4.18218324285	-0.207345418188	-0.0176338074103	-0.379253603778	-0.103880777469	-0.143559568441	-0.751524240808	-0.254831419617	0.690742087663	0.240809219587	0.32819710008	-0.38923589961	0.0156904868167	0.505202882285	0.0169239084799	0.373758290755	18.9900667893	11.6617241068	-15.1305273464
10	5.27874154244	4.54577450988	-1.38589811323	4.19753945726	-1.61037390297	0.887358552957	0.0328927771725	-0.394547062639	0.181568948576	-0.161376588738	-0.150152833721	0.110871347189	-0.820926661015	0.211875347016	-0.0853869912123	0.457159924344	-0.203115428229	0.0286901452748	0.236186439826	-0.00146560606911	0.331523172293	4.87648630721	13.2891116009	-19.3584333719
11	2.3164317696	-2.92709859324	-0.680321683876	6.62190508153	-0.681075872129	1.01496129139	0.019190596357	0.206005402776	-0.164792579492	-0.57666613663	-0.263861152658	0.918563262978	-0.523300704273	-0.901152821665	0.146248773886	0.806336668255	0.476432655709	-0.130878281661	0.938159723128	0.0295487355343	0.516237392279	-16.9667511676	15.5387188648	-8.96594226763
12	1.972047528	-2.63897294239	-1.30941409576	8.82391853128	3.5058910423	4.87436488546	-0.281893362584	-0.0907496986822	-0.092430009154	0.570748803932	0.307491803126	0.108311494742	0.0420939590954	-0.0437048483742	0.0399126132262	0.244296059286	0.0139099060761	-0.0141051662534	0.173817379907	0.0391667662957	0.270147705337	-3.41979566264	4.97183209421	1.45741295776
13	2.03872727802	-1.93307448825	-1.51969427425	3.83918624976	0.70684602413	1.87225567722	0.166252224687	0.392184279669	-0.0195975354294	-0.425055450701	-0.269287054366	0.726358822148	-1.16326444048	-1.41962578833	0.444172608545	0.685739110378	0.328194614063	-0.0685476932399	0.569247002547	-0.052259992524	0.331197432043	-13.2936427037	16.8807615106	-3.22253454605
14	5.50748963112	-0.743832474959	-1.98673849772	7.03087060651	1.82670231332	3.66335351534	-0.218190675142	0.295552643063	0.786710581343	-0.503282011239	0.258921064726	-0.22776277693	-0.569629593751	-0.167249669786	-0.0495581173587	1.02488930078	0.0466729498727	0.0519572680689	0.228606418855	0.050648947294	0.484119760996	-1.78330543922	25.0648621937	0.467251079666
15	6.40840539901	-1.29203969912	-0.184128301249	4.16093253667	-0.0255469357504	5.16275971319	-0.123753503757	0.00932960668212	-0.656013714505	0.157498684377	-0.0908725804965	0.431501883116	-0.74472972082	-1.23277916529	0.177100073948	0.405536074849	0.190227724403	0.0174640183116	0.48205690785	-0.0617623492411	0.378207702909	-13.1304099559	13.4450222843	1.59039359755
16	1.33154676723	-0.586818697194	-1.59653772827	2.59006472621	1.91950626902	2.97899949052	-0.146254021408	0.274931801512	-0.000528598881828	0.167312348627	-0.198856685103	0.436846192382	-0.627898464937	-1.18957840611	0.12884049026	0.518951935742	0.340371691519	-0.0372664718385	0.525480389966	-0.043762438053	0.349949566903	-12.1142444721	14.5869363556	1.1517085505
17	6.95366744652	-1.76107178275	3.72676731685	3.8543602641	3.27920235577	7.23356902697	-0.0994403275269	0.362970459731	-0.400068011143	-0.241567812744	0.198062647864	-0.947706428934	1.87253276084	0.858943252028	0.00706431645779	0.627494850211	0.0977069194075	0.0886030413306	0.31223242642	-0.00987668880417	0.473969527632	6.73095293332	-15.3958433469	-4.60262228142
18	6.0681070192	5.95447313178	-5.742180346	5.89561545802	-5.72946517926	5.60171740749	-0.458485785843	-0.243527836929	-0.927622871783	-0.132249320883	-0.150609324196	-1.11433279595	0.564353677405	0.665853987603	0.51393754732	0.345273932101	0.011192111708	0.0385335096316	0.223815965078	0.0232358660881	0.438312885241	5.20108155345	-8.24616990683	0.186011063393
19	6.63361505494	4.3253002624	-1.88185430169	3.9164059841	-2.58376858647	3.1247872832	0.131670846354	-0.408296696617	-0.139806768465	0.483681084069	0.0493095416013	-0.386339614946	-0.600880369571	0.524586143315	-0.12005013019	0.371273890164	-0.182930748677	-0.0536430542113	0.431648847617	0.0227128077825	0.297591071136	12.7534783694	12.1221458332	-6.38143426169

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 650 through 656 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 657 through 667 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 668 through 680 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 681 through 689 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 690 through 705 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 706 through 714 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 715 through 725 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 726 through 734 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 735 through 745 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 746 through 758 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 759 through 785 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 650 through 667 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 668 through 705 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 706 through 714 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 715 through 734 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 735 through 761 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 762 through 771 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 772 through 776 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 777 through 787 )

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