PDB-2pft: The Crystal Structure of Mouse Exo70 Reveals Unique Features of t...

ID or keywords:

Entry

Database: PDB / ID: 2pft

Title

The Crystal Structure of Mouse Exo70 Reveals Unique Features of the Mammalian Exocyst

Components

Exocytosis Protein

Keywords

ENDOCYTOSIS/EXOCYTOSIS / helix-turn-helix / ENDOCYTOSIS-EXOCYTOSIS COMPLEX

Function / homology

Function and homology information

Insulin processing / VxPx cargo-targeting to cilium / vesicle tethering involved in exocytosis / exocyst / regulation of entry of bacterium into host cell / positive regulation of mitotic cytokinetic process / growth cone membrane / protein transmembrane transport / membrane fission / Flemming body ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.25 Å

Authors

Moore, B.A. / Xu, Z.

Citation

Journal: J.Mol.Biol. / Year: 2007
Title: The crystal structure of mouse Exo70 reveals unique features of the mammalian exocyst.
Authors: Moore, B.A. / Robinson, H.H. / Xu, Z.

History

Deposition	Apr 5, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 22, 2007	Provider: repository / Type: Initial release
Revision 1.1	Dec 17, 2007	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Nov 16, 2011	Group: Atomic model
Revision 1.4	Oct 18, 2017	Group: Refinement description / Category: software
Revision 1.5	Feb 21, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2pft.cif.gz	122.1 KB	Display	PDBx/mmCIF format
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Others	Other downloads

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Validation report

Summary document	2pft_validation.pdf.gz	428.6 KB	Display	wwPDB validaton report
Full document	2pft_full_validation.pdf.gz	440.3 KB	Display
Data in XML	2pft_validation.xml.gz	22.4 KB	Display
Data in CIF	2pft_validation.cif.gz	31.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pf/2pft ftp://data.pdbj.org/pub/pdb/validation_reports/pf/2pft	HTTPS FTP

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Related structure data

Related structure data	2pfvC C: citing same article (ref.)
Similar structure data	495 2b1e-d 3vp9-1 3pqh-d 2b7m-2 4i0k-1 2pfv-d 3syv-2 1f02-1 1wmg-d 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	#60 - Dec 2004 Ubiquitin similarity (1)

Deposited unit

A: Exocytosis Protein

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	61.520, 61.520, 294.730
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21

Components on special symmetry positions

ID	Model	Components
1	1	A-812- HOH

#1: Protein	Exocytosis Protein Mass: 65555.477 Da / Num. of mol.: 1 / Fragment: Residues 85-653 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Exoc7 / Plasmid: pSJ7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q3TIP4, UniProt: O35250*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Exocytosis Protein

Mass: 65555.477 Da / Num. of mol.: 1 / Fragment: Residues 85-653
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mus musculus (house mouse) / Gene: Exoc7 / Plasmid: pSJ7 / Species (production host): Escherichia coli / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q3TIP4, UniProt: O35250*PLUS

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.46 Å³/Da / Density % sol: 49.9 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Precipitant in drop: 10% ethylene glycol, 5% PEG 8000, 0.01M magnesium chloride, 0.1M HEPES Precipitant in well: 10% ethylene glycol, 8% PEG 8000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, ...Details: Precipitant in drop: 10% ethylene glycol, 5% PEG 8000, 0.01M magnesium chloride, 0.1M HEPES Precipitant in well: 10% ethylene glycol, 8% PEG 8000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

Crystal

Density Matthews: 2.46 Å³/Da / Density % sol: 49.9 %

Crystal grow

Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Precipitant in drop: 10% ethylene glycol, 5% PEG 8000, 0.01M magnesium chloride, 0.1M HEPES Precipitant in well: 10% ethylene glycol, 8% PEG 8000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, ...

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	77	1
2		1
3		1

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-D / Wavelength: 0.97926,0.97942,0.95660

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 19, 2006 / Details: Adjustable focusing mirrors in K-B geometry

Radiation

Monochromator: Si(111) Double Crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97926	1
2	0.97942	1
3	0.9566	1

Reflection

D res high: 2.5 Å / D res low: 50 Å

Redundancy (%)	ID	Av σ(I) over netI	Number	R_merge(I) obs	Χ²	Num. obs	% possible obs
6.2	1	15.4	144140	0.079	2.76	23320	98.6
5.7	2	15.3	131313	0.069	2.04	23003	97.1
5.4	3	14.7	119444	0.069	1.91	22284	93.4

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
5.38	50	98	1	0.07	6.861	5.8
4.27	5.38	99.3	1	0.072	4.682	6.1
3.73	4.27	100	1	0.069	3.382	6.4
3.39	3.73	100	1	0.081	3.049	6.4
3.15	3.39	100	1	0.101	2.515	6.6
2.96	3.15	100	1	0.115	1.712	6.7
2.82	2.96	100	1	0.14	1.38	6.6
2.69	2.82	100	1	0.179	1.227	6.4
2.59	2.69	99.6	1	0.253	1.27	6
2.5	2.59	89.2	1	0.297	0.982	4.6
5.38	50	98.1	2	0.052	3.566	5.6
4.27	5.38	99.4	2	0.062	2.982	6
3.73	4.27	99.9	2	0.063	2.439	6.2
3.39	3.73	100	2	0.079	2.4	6.3
3.15	3.39	99.9	2	0.105	1.939	6.4
2.96	3.15	99.9	2	0.135	1.431	6.5
2.82	2.96	100	2	0.182	1.244	6.3
2.69	2.82	99.5	2	0.236	1.126	5.6
2.59	2.69	96.5	2	0.318	1.104	4.5
2.5	2.59	77.5	2	0.365	1.117	3
5.38	50	97.9	3	0.05	2.854	5.5
4.27	5.38	99.6	3	0.062	2.704	5.9
3.73	4.27	99.8	3	0.067	2.371	6
3.39	3.73	99.6	3	0.089	2.265	6.2
3.15	3.39	99.8	3	0.13	1.814	6.3
2.96	3.15	99.9	3	0.176	1.304	6.2
2.82	2.96	99.7	3	0.229	1.09	5.6
2.69	2.82	94.1	3	0.295	1.015	4.6
2.59	2.69	83.1	3	0.386	0.991	3.3
2.5	2.59	59.2	3	0.423	0.972	2.3

Reflection

Resolution: 2.25→46.84 Å / Num. all: 31423 / Num. obs: 30334 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Redundancy: 4.2 % / B_iso Wilson estimate: 40.4 Å² / Limit h max: 24 / Limit h min: 0 / Limit k max: 24 / Limit k min: 0 / Limit l max: 133 / Limit l min: 0 / Observed criterion F max: 127192.55 / Observed criterion F min: 0.32 / R_merge(I) obs: 0.054 / Χ²: 1.26 / Net I/σ(I): 15.8

Reflection shell

Resolution: 2.25→2.33 Å / Redundancy: 3.1 % / R_merge(I) obs: 0.416 / Num. unique all: 2448 / Χ²: 1.093 / % possible all: 77.7

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Phasing

Phasing

Method:

MAD

Phasing MAD set

ID	R cullis acentric	R cullis centric	Highest resolution (Å)	Lowest resolution (Å)	Reflection acentric	Reflection centric
ISO_1	0	0	2.5	46.9	19471	3780
ISO_2	0.382	0.345	2.5	46.9	19134	3700
ISO_3	0.595	0.57	2.5	46.9	18345	3614
ANO_1	0.514	0	2.5	46.9	19069	0
ANO_2	0.693	0	2.5	46.9	17981	0
ANO_3	0.796	0	2.5	46.9	16581	0

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Reflection acentric	Reflection centric
ISO_1	10.89-46.9	0	0	159	157
ISO_1	7.81-10.89	0	0	339	187
ISO_1	6.4-7.81	0	0	489	194
ISO_1	5.56-6.4	0	0	578	195
ISO_1	4.98-5.56	0	0	687	189
ISO_1	4.55-4.98	0	0	752	180
ISO_1	4.22-4.55	0	0	823	200
ISO_1	3.94-4.22	0	0	889	192
ISO_1	3.72-3.94	0	0	970	201
ISO_1	3.53-3.72	0	0	1021	188
ISO_1	3.37-3.53	0	0	1083	190
ISO_1	3.22-3.37	0	0	1108	197
ISO_1	3.1-3.22	0	0	1179	202
ISO_1	2.99-3.1	0	0	1268	179
ISO_1	2.89-2.99	0	0	1258	207
ISO_1	2.79-2.89	0	0	1322	198
ISO_1	2.71-2.79	0	0	1386	191
ISO_1	2.64-2.71	0	0	1414	195
ISO_1	2.57-2.64	0	0	1455	175
ISO_1	2.5-2.57	0	0	1291	163
ANO_1	10.89-46.9	0.329	0	149	0
ANO_1	7.81-10.89	0.369	0	331	0
ANO_1	6.4-7.81	0.299	0	488	0
ANO_1	5.56-6.4	0.295	0	574	0
ANO_1	4.98-5.56	0.368	0	678	0
ANO_1	4.55-4.98	0.47	0	739	0
ANO_1	4.22-4.55	0.432	0	808	0
ANO_1	3.94-4.22	0.455	0	875	0
ANO_1	3.72-3.94	0.475	0	960	0
ANO_1	3.53-3.72	0.546	0	1004	0
ANO_1	3.37-3.53	0.553	0	1077	0
ANO_1	3.22-3.37	0.567	0	1103	0
ANO_1	3.1-3.22	0.59	0	1175	0
ANO_1	2.99-3.1	0.657	0	1267	0
ANO_1	2.89-2.99	0.699	0	1255	0
ANO_1	2.79-2.89	0.768	0	1320	0
ANO_1	2.71-2.79	0.806	0	1381	0
ANO_1	2.64-2.71	0.937	0	1394	0
ANO_1	2.57-2.64	0.925	0	1396	0
ANO_1	2.5-2.57	0.952	0	1095	0
ISO_2	10.89-46.9	0.331	0.365	155	155
ISO_2	7.81-10.89	0.342	0.251	337	185
ISO_2	6.4-7.81	0.181	0.17	489	193
ISO_2	5.56-6.4	0.172	0.164	578	195
ISO_2	4.98-5.56	0.203	0.188	686	189
ISO_2	4.55-4.98	0.241	0.281	751	178
ISO_2	4.22-4.55	0.242	0.272	823	197
ISO_2	3.94-4.22	0.249	0.308	889	192
ISO_2	3.72-3.94	0.27	0.311	970	201
ISO_2	3.53-3.72	0.274	0.325	1021	188
ISO_2	3.37-3.53	0.328	0.389	1082	190
ISO_2	3.22-3.37	0.371	0.45	1105	197
ISO_2	3.1-3.22	0.464	0.546	1178	201
ISO_2	2.99-3.1	0.521	0.706	1268	178
ISO_2	2.89-2.99	0.612	0.717	1256	207
ISO_2	2.79-2.89	0.71	0.789	1320	197
ISO_2	2.71-2.79	0.772	0.87	1378	187
ISO_2	2.64-2.71	0.438	0.873	1398	185
ISO_2	2.57-2.64	0.825	0.897	1378	160
ISO_2	2.5-2.57	0.858	0.908	1072	125
ANO_2	10.89-46.9	0.471	0	149	0
ANO_2	7.81-10.89	0.489	0	331	0
ANO_2	6.4-7.81	0.363	0	487	0
ANO_2	5.56-6.4	0.411	0	576	0
ANO_2	4.98-5.56	0.528	0	678	0
ANO_2	4.55-4.98	0.644	0	731	0
ANO_2	4.22-4.55	0.617	0	802	0
ANO_2	3.94-4.22	0.647	0	860	0
ANO_2	3.72-3.94	0.66	0	950	0
ANO_2	3.53-3.72	0.743	0	996	0
ANO_2	3.37-3.53	0.746	0	1064	0
ANO_2	3.22-3.37	0.786	0	1088	0
ANO_2	3.1-3.22	0.793	0	1167	0
ANO_2	2.99-3.1	0.865	0	1259	0
ANO_2	2.89-2.99	0.881	0	1250	0
ANO_2	2.79-2.89	0.92	0	1303	0
ANO_2	2.71-2.79	0.931	0	1295	0
ANO_2	2.64-2.71	0.974	0	1228	0
ANO_2	2.57-2.64	0.978	0	1096	0
ANO_2	2.5-2.57	0.983	0	671	0
ISO_3	10.89-46.9	0.512	0.528	155	152
ISO_3	7.81-10.89	0.506	0.546	338	185
ISO_3	6.4-7.81	0.509	0.474	489	194
ISO_3	5.56-6.4	0.538	0.566	577	195
ISO_3	4.98-5.56	0.513	0.545	686	187
ISO_3	4.55-4.98	0.492	0.492	752	178
ISO_3	4.22-4.55	0.514	0.521	823	199
ISO_3	3.94-4.22	0.504	0.567	889	192
ISO_3	3.72-3.94	0.541	0.585	967	200
ISO_3	3.53-3.72	0.518	0.554	1019	187
ISO_3	3.37-3.53	0.581	0.602	1075	189
ISO_3	3.22-3.37	0.629	0.685	1106	197
ISO_3	3.1-3.22	0.699	0.712	1178	202
ISO_3	2.99-3.1	0.753	0.851	1266	179
ISO_3	2.89-2.99	0.781	0.875	1255	204
ISO_3	2.79-2.89	0.845	0.93	1317	191
ISO_3	2.71-2.79	0.864	0.96	1308	173
ISO_3	2.64-2.71	0.876	0.959	1257	163
ISO_3	2.57-2.64	0.865	0.921	1135	151
ISO_3	2.5-2.57	0.894	1.005	753	96
ANO_3	10.89-46.9	0.505	0	144	0
ANO_3	7.81-10.89	0.619	0	330	0
ANO_3	6.4-7.81	0.51	0	486	0
ANO_3	5.56-6.4	0.513	0	571	0
ANO_3	4.98-5.56	0.669	0	676	0
ANO_3	4.55-4.98	0.776	0	731	0
ANO_3	4.22-4.55	0.746	0	791	0
ANO_3	3.94-4.22	0.76	0	851	0
ANO_3	3.72-3.94	0.802	0	932	0
ANO_3	3.53-3.72	0.851	0	985	0
ANO_3	3.37-3.53	0.856	0	1047	0
ANO_3	3.22-3.37	0.88	0	1088	0
ANO_3	3.1-3.22	0.904	0	1170	0
ANO_3	2.99-3.1	0.943	0	1257	0
ANO_3	2.89-2.99	0.97	0	1230	0
ANO_3	2.79-2.89	0.976	0	1236	0
ANO_3	2.71-2.79	0.969	0	1096	0
ANO_3	2.64-2.71	0.978	0	884	0
ANO_3	2.57-2.64	0.991	0	661	0
ANO_3	2.5-2.57	0.992	0	415	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	-31.791	-22.349	-0.665	SE	60.58	0.91
2	-7.811	-42.177	-10.244	SE	56.8	0.94
3	16.393	-31.502	-14.809	SE	57.67	0.94
4	-35.063	-41.92	-3.793	SE	55.5	1.11
5	-10.793	-23.465	-42.746	SE	71.71	1.05
6	-40.086	-28.025	-21.986	SE	86.26	1.08
7	-49.165	-2.637	-28.712	SE	79.7	0.88
8	-34.492	-21.508	-23.78	SE	79.51	0.89
9	-7.261	-11.69	-30.628	SE	71.38	0.58
10	-5.524	-27.151	-7.297	SE	100.33	0.84

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
SOLOMON		phasing
CNS	1.2	refinement
PDB_EXTRACT	2	data extraction
Blu-Ice	(Custom)	data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MAD / Resolution: 2.25→46.84 Å / R_factor R_free error: 0.008 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 127010.656 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.285	1435	5 %	RANDOM
R_work	0.235	-	-	-
all	-	32008	-	-
obs	-	28804	90 %	-

Solvent computation

Solvent model: FLAT MODEL / B_sol: 57.814 Å² / k_sol: 0.35 e/Å³

Displacement parameters

B_iso max: 98.02 Å² / B_iso mean: 54.8 Å² / B_iso min: 29.02 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.06 Å²	0 Å²	0 Å²
2-	-	2.06 Å²	0 Å²
3-	-	-	-4.11 Å²

Refine analyze

	Free	Obs
Luzzati coordinate error	0.4 Å	0.32 Å
Luzzati d res low	-	5 Å
Luzzati sigma a	0.38 Å	0.28 Å
Luzzati d res high	-	2.25

Refinement step

Cycle: LAST / Resolution: 2.25→46.84 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4098	0	0	170	4268

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target
X-RAY DIFFRACTION	x_bond_d	0.006
X-RAY DIFFRACTION	x_angle_deg	1.1
X-RAY DIFFRACTION	x_torsion_deg	17.9
X-RAY DIFFRACTION	x_torsion_impr_deg	0.85
X-RAY DIFFRACTION	x_mcbond_it	1.43	1.5
X-RAY DIFFRACTION	x_mcangle_it	2.36	2
X-RAY DIFFRACTION	x_scbond_it	2.17	2
X-RAY DIFFRACTION	x_scangle_it	3.23	2.5

LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)	R_factor R_free	Num. reflection R_free	% reflection R_free (%)	R_factor R_work	Num. reflection R_work	R_factor R_free error	Num. reflection all	Num. reflection obs	% reflection obs (%)
2.25-2.35	0.378	134	4.8	0.31	2643	0.033	3933	2777	70.6
2.35-2.48	0.362	159	5	0.283	2992	0.029	3936	3151	80.1
2.48-2.63	0.325	198	5.8	0.283	3190	0.023	3907	3388	86.7
2.63-2.83	0.314	191	5.3	0.259	3433	0.023	3936	3624	92
2.83-3.12	0.346	162	4.3	0.276	3610	0.027	3992	3772	94.5
3.12-3.57	0.314	199	5.2	0.254	3661	0.022	4002	3860	96.5
3.57-4.5	0.238	193	4.8	0.212	3791	0.017	4044	3984	98.5
4.5-46.83	0.274	199	4.7	0.219	4049	0.019	4287	4248	99.1

Xplor file

Refine-ID	Serial no	Param file	Topol file
X-RAY DIFFRACTION	1	protein_rep.param	protein.top
X-RAY DIFFRACTION	2	water_rep.param

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Feb 9, 2022. New format data for meta-information of EMDB entries

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