PDB-9bli: Crystal structure of Actin capping protein in complex with a frag...

ID or keywords:

Entry

Database: PDB / ID: 9bli

Title

Crystal structure of Actin capping protein in complex with a fragment of Legionella pneumophila RavB

Components

F-actin-capping protein subunit alpha-1
F-actin-capping protein subunit beta isoforms 1 and 2
Integrase

Keywords

PROTEIN BINDING / ACTIN CAPPING PROTEIN / BARBED END REGULATION / CONFORMATIONAL CHANGE / CELL MOTILITY / ACTIN CAPPING / ACTIN-BINDING / CYTOSKELETON / SECRETED BACTERIAL EFFECTOR PROTEIN

Function / homology

Function and homology information

Advanced glycosylation endproduct receptor signaling / RHOD GTPase cycle / RHOF GTPase cycle / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-independent Golgi-to-ER retrograde traffic / Factors involved in megakaryocyte development and platelet production / COPI-mediated anterograde transport / negative regulation of filopodium assembly / sperm head-tail coupling apparatus / F-actin capping protein complex ...
Similarity search - Function

Biological species

Gallus gallus (chicken)

Legionella pneumophila subsp. pneumophila (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Ye, J.S. / Majumdar, A. / Tomchick, D.R. / Tagliabracci, V.S.

Funding support

United States, 5items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	DP2GM137419	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	K99GM147532	United States
Robert A. Welch Foundation	I-1911	United States
Robert A. Welch Foundation	I-1704	United States
Howard Hughes Medical Institute (HHMI)		United States

Citation

Journal: To Be Published
Title: Bacterial ubiquitin ligase engineered for small molecule and protein target identification
Authors: Ye, J.S. / Majumdar, A. / Park, B. / Black, M.H. / Hsieh, T.-S. / Osinski, A. / Servage, K.A. / Kulkarni, K. / Naidoo, J. / Alto, N.M. / Stratton, M.M. / Ready, J.M. / Pawlowski, K. / ...

History

Deposition	Apr 30, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 7, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9bli.cif.gz	393.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9bli.ent.gz	267.2 KB	Display	PDB format
PDBx/mmJSON format	9bli.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9bli_validation.pdf.gz	445.2 KB	Display	wwPDB validaton report
Full document	9bli_full_validation.pdf.gz	446.5 KB	Display
Data in XML	9bli_validation.xml.gz	25.7 KB	Display
Data in CIF	9bli_validation.cif.gz	33.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bl/9bli ftp://data.pdbj.org/pub/pdb/validation_reports/bl/9bli	HTTPS FTP

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Related structure data

Related structure data	9blhC C: citing same article (ref.)
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

Deposited unit

A: F-actin-capping protein subunit alpha-1

B: F-actin-capping protein subunit beta isoforms 1 and 2

C: Integrase

hetero molecules

66 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	66.502, 55.322, 77.900
Angle α, β, γ (deg.)	90.000, 107.080, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	F-actin-capping protein subunit alpha-1 / Beta-actinin subunit I / CapZ 36/32 Mass: 33001.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: CAPZA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P13127
#2: Protein	F-actin-capping protein subunit beta isoforms 1 and 2 / Beta-actinin subunit II / CapZ 36/32 / CapZ B1 and B2 Mass: 27893.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: CAPZB / Production host: Escherichia coli (E. coli) / References: UniProt: P14315
#3: Protein/peptide	Integrase Mass: 4930.744 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria) Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg0030 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZZI0
#4: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH₂O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	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: 2.08 Å³/Da / Density % sol: 40.89 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 10 mM Tris pH 8.0, 0.2 M ammonium formate, 0.15 M NaCl, 21% w/v PEG 3350, 30% ethylene glycol

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5418 Å

Detector

Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Oct 5, 2023

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 2→50 Å / Num. obs: 35564 / % possible obs: 96.7 % / Redundancy: 9.3 % / B_iso Wilson estimate: 25.48 Å² / CC_1/2: 0.994 / CC star: 0.999 / R_merge(I) obs: 0.124 / R_pim(I) all: 0.039 / R_rim(I) all: 0.13 / Χ²: 0.97 / Net I/σ(I): 6.8 / Num. measured all: 330215

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2-2.03	1.3	0.359	1036	0.791	0.94	0.345	0.499	1.221	56.6
2.03-2.07	2.1	0.332	1550	0.818	0.949	0.249	0.419	1.068	85.4
2.07-2.11	2.8	0.334	1735	0.837	0.955	0.218	0.403	0.994	93.6
2.11-2.15	3.4	0.327	1774	0.878	0.967	0.191	0.381	0.982	98.1
2.15-2.2	4.3	0.334	1796	0.899	0.973	0.175	0.379	1.015	99.6
2.2-2.25	5.3	0.316	1823	0.929	0.981	0.148	0.35	1.054	99.9
2.25-2.31	6.7	0.325	1835	0.954	0.988	0.133	0.352	1.059	100
2.31-2.37	8.1	0.331	1835	0.959	0.99	0.122	0.353	1.028	100
2.37-2.44	9.2	0.297	1840	0.975	0.994	0.102	0.315	0.998	100
2.44-2.52	10.2	0.289	1843	0.981	0.995	0.094	0.304	1.006	100
2.52-2.61	11.1	0.258	1807	0.985	0.996	0.08	0.27	0.974	100
2.61-2.71	12	0.238	1838	0.988	0.997	0.071	0.249	0.988	100
2.71-2.84	12.8	0.219	1827	0.992	0.998	0.064	0.229	0.974	100
2.84-2.99	13.2	0.192	1856	0.994	0.999	0.055	0.199	0.954	100
2.99-3.17	13.4	0.158	1817	0.996	0.999	0.045	0.164	0.95	100
3.17-3.42	13.4	0.122	1867	0.997	0.999	0.035	0.127	0.964	100
3.42-3.76	13.3	0.094	1835	0.998	0.999	0.026	0.097	0.98	100
3.76-4.31	13.2	0.076	1870	0.998	1	0.022	0.079	0.923	100
4.31-5.43	12.8	0.068	1856	0.999	1	0.019	0.07	0.917	100
5.43-50	11.5	0.067	1924	0.999	1	0.021	0.07	0.895	100

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
HKL-3000		data scaling
HKL-3000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→44.41 Å / SU ML: 0.2022 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.0127
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2076	2550	7.28 %
R_work	0.1802	32496	-
obs	0.1822	35046	95.21 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 29.61 Å²

Refinement step

Cycle: LAST / Resolution: 2→44.41 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4391	0	9	181	4581

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0049	4503
X-RAY DIFFRACTION	f_angle_d	0.7123	6088
X-RAY DIFFRACTION	f_chiral_restr	0.0453	658
X-RAY DIFFRACTION	f_plane_restr	0.0079	801
X-RAY DIFFRACTION	f_dihedral_angle_d	14.0785	1697

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 (%)
2-2.04	0.3623	61	0.2632	769	X-RAY DIFFRACTION	40.73
2.04-2.08	0.2471	121	0.2284	1556	X-RAY DIFFRACTION	82.37
2.08-2.13	0.2535	136	0.2153	1736	X-RAY DIFFRACTION	92.63
2.13-2.18	0.2677	145	0.2052	1837	X-RAY DIFFRACTION	97.92
2.18-2.23	0.2286	149	0.194	1903	X-RAY DIFFRACTION	99.81
2.23-2.29	0.2164	147	0.1817	1876	X-RAY DIFFRACTION	100
2.29-2.36	0.2272	147	0.1873	1860	X-RAY DIFFRACTION	100
2.36-2.43	0.2094	150	0.1821	1908	X-RAY DIFFRACTION	100
2.43-2.52	0.2036	148	0.184	1889	X-RAY DIFFRACTION	100
2.52-2.62	0.2182	148	0.1843	1885	X-RAY DIFFRACTION	100
2.62-2.74	0.2228	146	0.1869	1875	X-RAY DIFFRACTION	100
2.74-2.89	0.2479	151	0.1988	1914	X-RAY DIFFRACTION	100
2.89-3.07	0.2078	149	0.2009	1892	X-RAY DIFFRACTION	100
3.07-3.3	0.2335	149	0.1889	1902	X-RAY DIFFRACTION	100
3.3-3.63	0.2069	146	0.186	1871	X-RAY DIFFRACTION	100
3.64-4.16	0.168	152	0.1615	1935	X-RAY DIFFRACTION	100
4.16-5.24	0.162	149	0.1403	1900	X-RAY DIFFRACTION	99.95
5.24-44.41	0.2007	156	0.1708	1988	X-RAY DIFFRACTION	99.95

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	1.93580283634	0.564886321493	0.264057810169	1.57904664039	-0.0247236557805	1.2476782021	0.0762581317708	-0.445646927139	-0.280706142595	0.283136214282	-0.0780636271223	0.119032373221	0.10564456384	-0.207526545348	0.0289297500166	0.226584981412	-0.0207430999951	0.0254307959906	0.263259241505	0.0305899674459	0.233031108029	-30.9067216961	-16.9498414416	-5.45338221575
2	0.596495247793	0.241863845532	-0.210048642402	3.62299790175	0.0025674587745	2.54341504764	0.174868268029	0.00430866228013	-0.196937578004	0.0266458453019	0.00630284613163	0.0774192282466	0.212751612464	-0.0329968926481	-0.129277654066	0.206954575095	0.00197326359746	-0.0393548778266	0.207557613612	-0.000316725070197	0.283727998388	-42.8832390163	-27.3567756006	-24.2652315464
3	3.57403357211	0.61933778348	0.152099870252	2.66299369889	-0.477757794373	2.03879878113	0.0479132303265	-0.0405471692139	-0.242968044415	-0.0613092601339	0.0118367737354	0.270521401706	0.0183639896897	-0.353251979194	-0.0562975953013	0.226441668357	0.00674801185967	-0.0240872322263	0.234257731136	-0.0106169974359	0.22862721526	-47.2458005565	-17.7956679302	-34.1558229469
4	1.06808761692	0.71011273756	0.462508518785	1.1199500489	0.193119582652	0.532011925837	-0.0222315040244	0.0411090263469	0.0635548384711	-0.120635524555	0.00159563587888	0.139717965503	-0.051353921289	-0.00674513167084	0.0203262545371	0.190590762021	0.0348737993236	0.0209428680107	0.193057371613	-0.0125951045312	0.151918023961	-33.2554009579	-1.35472821119	-29.4324399114
5	1.90018072257	-0.29841269385	1.27446380405	0.858794221799	-0.786923800477	2.06838226579	-0.0957264598941	-0.0833645471992	-0.0424685281416	0.0873664455329	0.00627155180576	-0.187000721369	0.0113589263498	0.100336673205	0.0585748616613	0.221833581194	0.0118391912864	0.025682085655	0.206572286793	-0.00500532033979	0.247365061891	-15.5441246605	-11.1819330388	-6.00228192739
6	1.39624681168	-0.0566750568643	0.657911438357	2.29025937206	-1.15368897737	4.32236457777	-0.0752019733029	-0.124944428336	0.0297376692644	0.247806282169	0.139501230934	0.305395603739	-0.181651310337	-0.550668750235	-0.0457033093433	0.205000161995	0.00633047128963	0.0135898176711	0.262222349318	0.0135833421078	0.230179396213	-26.619411563	-3.67514583072	-5.61852664238
7	0.683844047653	0.448082570761	0.317086851929	1.21930735848	0.235470245944	1.12535898049	-0.0109500897807	-0.145648130506	0.132991665853	0.159144921262	-0.0118535882678	0.0670180943697	-0.0529658374519	-0.0533859734148	0.000817243392674	0.22289258628	0.00706800651662	0.0381418613702	0.221277825435	0.0171759597692	0.228904347525	-18.3503559815	8.57746772622	-1.23637197991
8	3.21936381651	0.338631397681	-0.199045308933	1.71574640302	0.175841925597	0.711657920975	-0.0882169594214	-0.445961462166	0.142895453858	0.201945561285	0.056213345885	0.0503403102388	-0.220938728152	0.0650241452415	0.0058827777499	0.285868291077	0.00851824053197	-0.000685660992907	0.244698209236	-0.0120225750219	0.222667351637	-13.7364157404	16.1886044746	6.11444597903
9	1.12830318414	0.497492545843	0.485612190733	1.38555007229	0.711466443887	1.71303003725	-0.0824976994313	-0.0557092205766	0.11339735695	0.0270738270473	-0.0245133090925	-0.0752195384608	-0.127500728685	0.0777410932858	0.109552261789	0.190025803123	-0.0120946846676	0.00919205094851	0.198304678298	0.000497854836437	0.189571234804	-10.3633470869	16.3555487701	-9.78228037284
10	2.1827954827	1.12046140167	1.50484388595	0.57997613704	0.724807228503	1.15788150243	0.0540289936715	0.0891052975071	-0.35946605053	0.0802395984347	0.0676305149591	-0.0397081812713	0.0136242819038	0.0796700834693	-0.108579389765	0.219303894446	-0.00337886804366	0.0243660295686	0.221487693868	-0.00181826100953	0.197217228413	-5.91533705039	8.41518721221	-10.7786838303
11	2.85153416737	0.705774646136	1.07564332552	0.410712786051	0.612554341962	0.931726367159	-0.125557126476	0.307159098904	0.10362431958	-0.0549756229538	0.100635493521	0.00452414998823	-0.105508857292	0.164512768258	0.0306128989002	0.237307263531	-0.0314347180271	0.0140391532339	0.218288534105	0.0227378035014	0.217663558794	-10.795538308	6.56922651786	-17.1231918985
12	1.59308844286	1.3811170157	0.871016219393	1.33712258458	0.627865461433	0.578766464871	-0.133047547371	0.19773979947	-0.0401180300681	-0.157884909725	0.129186031674	-0.0937733623213	-0.122016129902	0.158860040769	-0.0142079276004	0.23620398908	-0.0240204280123	0.0207002556679	0.247396983826	0.00738147600833	0.216478697779	-13.5979770957	4.91193015606	-25.0893879099
13	4.24045149361	1.81466988488	0.667606992584	3.69230464601	0.171549123017	2.63337330545	0.464616991053	0.277328550406	-0.600951151235	-0.261214610664	0.3739258374	0.0360344661677	0.0710603232929	-0.269208706536	-0.804490480834	0.251716184217	-0.00795968877507	0.00117358624419	0.333574637838	0.0177394416884	0.416983717139	-10.6093991381	-7.50819217199	-13.4240544018
14	7.86159903592	0.10570103013	1.34071269525	4.86269466479	-0.368045027088	7.4564673754	0.358543270834	-0.369584411174	-0.877068537585	0.626233944302	-0.140825241511	-0.151067866724	0.537533338259	0.0372078576441	-0.158350885042	0.330524964474	-0.00435249487251	-0.0303006680536	0.334564394189	0.0474603185315	0.327669418284	-7.77900754831	-3.13154875214	-5.45215910714
15	4.66427630638	1.10433603331	-0.794559365933	3.35516457278	0.165692992001	5.27770284901	-0.110467078939	-0.572367196544	-0.0402086675138	0.201204599263	0.0379508341312	-0.61245568959	0.39612089896	0.598869397534	0.0154176114281	0.36606861886	0.109319967247	-0.0271620102375	0.268230790424	0.00547717065882	0.286994578338	-13.1546238824	3.2135920456	7.36987738562
16	1.07041789181	-0.375049895297	-0.498059144128	5.67992695119	-0.352901277421	0.294599071775	0.20649382467	-0.204150487792	-0.160505181023	-0.370907340069	0.0510174201928	-0.203784036373	0.177142722975	-0.0840142578021	-0.197079652941	0.316850409129	0.0274499532555	0.0549523502175	0.343906151599	0.00495060955357	0.349934871718	-25.0890057332	-1.76704699513	7.60133510068

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 3 through 60 )	A	A	3 - 60	1 - 58
2	2	chain 'A' and (resid 61 through 117 )	A	A	61 - 117	59 - 115
3	3	chain 'A' and (resid 118 through 151 )	A	A	118 - 151	116 - 149
4	4	chain 'A' and (resid 152 through 276 )	A	A	152 - 276	150 - 274
5	5	chain 'B' and (resid -3 through 17 )	B	D	-3 - 17	1 - 21
6	6	chain 'B' and (resid 18 through 31 )	B	D	18 - 31	22 - 35
7	7	chain 'B' and (resid 32 through 70 )	B	D	32 - 70	36 - 74
8	8	chain 'B' and (resid 71 through 90 )	B	D	71 - 90	75 - 94
9	9	chain 'B' and (resid 91 through 144 )	B	D	91 - 144	95 - 148
10	10	chain 'B' and (resid 145 through 162 )	B	D	145 - 162	149 - 166
11	11	chain 'B' and (resid 163 through 208 )	B	D	163 - 208	167 - 212
12	12	chain 'B' and (resid 209 through 244 )	B	D	209 - 244	213 - 248
13	13	chain 'C' and (resid 115 through 119 )	C	F	115 - 119	1 - 5
14	14	chain 'C' and (resid 120 through 124 )	C	F	120 - 124	6 - 10
15	15	chain 'C' and (resid 125 through 132 )	C	F	125 - 132	11 - 18
16	16	chain 'C' and (resid 133 through 139 )	C	F	133 - 139	19 - 25

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News

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