PDB-2oex: Structure of ALIX/AIP1 V Domain

ID or keywords:

Entry

Database: PDB / ID: 2oex

Title

Structure of ALIX/AIP1 V Domain

Components

Programmed cell death 6-interacting protein

Keywords

PROTEIN TRANSPORT /

Coiled-coil

Function / homology

Function and homology information

proteinase activated receptor binding / actomyosin contractile ring assembly / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / regulation of extracellular exosome assembly /

viral budding / extracellular exosome biogenesis / maintenance of epithelial cell apical/basal polarity / positive regulation of extracellular exosome assembly /

regulation of membrane permeability / regulation of centrosome duplication ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.58 Å

Authors

Fisher, R.D. / Zhai, Q. / Robinson, H. / Hill, C.P.

Citation

Journal: Cell(Cambridge,Mass.) / Year: 2007
Title: Structural and Biochemical Studies of ALIX/AIP1 and Its Role in Retrovirus Budding
Authors: Fisher, R.D. / Chung, H.Y. / Zhai, Q. / Robinson, H. / Sundquist, W.I. / Hill, C.P.

History

Deposition	Jan 1, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 27, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4	Dec 27, 2023	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2oex.cif.gz	282.2 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oe/2oex ftp://data.pdbj.org/pub/pdb/validation_reports/oe/2oex	HTTPS FTP

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Related structure data

Related structure data	2oevC 2oewC C: citing same article (ref.)
Similar structure data	3p4g-d 5xwx-d 5odu-d 4ko8-d 6b27-d 4es9-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	#28 - Apr 2002 Anthrax Toxin similarity (1) #141 - Sep 2011 O-GlcNAc Transferase similarity (1) #44 - Aug 2003 Calmodulin similarity (1) #56 - Aug 2004 Caspases similarity (1) #195 - Mar 2016 RAF Protein Kinases similarity (1) #196 - Apr 2016 Lead Poisoning similarity (1)

Deposited unit

A: Programmed cell death 6-interacting protein

B: Programmed cell death 6-interacting protein

79.3 kDa, 2 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)	63.861, 50.049, 130.171
Angle α, β, γ (deg.)	90.00, 101.13, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Programmed cell death 6-interacting protein / PDCD6-interacting protein / ALG-2-interacting protein 1 / Hp95 Mass: 39670.109 Da / Num. of mol.: 2 / Fragment: V Domain, residues 359-702 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD6IP, AIP1, ALIX, KIAA1375 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon + (RIL) / References: UniProt: Q8WUM4
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Programmed cell death 6-interacting protein / PDCD6-interacting protein / ALG-2-interacting protein 1 / Hp95

Mass: 39670.109 Da / Num. of mol.: 2 / Fragment: V Domain, residues 359-702
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: PDCD6IP, AIP1, ALIX, KIAA1375 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon + (RIL) / References: UniProt: Q8WUM4

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.57 Å³/Da / Density % sol: 52.21 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 14% PEG 3350, 0.16M magnesium formate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		1

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X29A / Wavelength: 0.9792 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 9, 2005

Radiation

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

Radiation wavelength

Wavelength: 0.9792 Å / Relative weight: 1

Reflection

D res high: 2.6 Å / D res low: 50 Å

ID	Av σ(I) over netI	Number	R_merge(I) obs	Χ²	Num. obs	% possible obs
1	13.2	77110	0.078	1.02	23601	92.4
2	11.7	146369	0.106	0.95	22229	89.8

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared
5.6	50	99.7	1	0.057	1.07
4.45	5.6	99.7	1	0.062	0.952
3.88	4.45	99.8	1	0.075	1.001
3.53	3.88	99.3	1	0.089	1.283
3.28	3.53	98.9	1	0.1	1.088
3.08	3.28	97.4	1	0.114	1.002
2.93	3.08	96.4	1	0.132	1.039
2.8	2.93	89.9	1	0.162	0.961
2.69	2.8	78.2	1	0.203	0.762
2.6	2.69	64	1	0.204	0.749
5.6	50	99.5	2	0.081	1.042
4.45	5.6	100	2	0.097	1.018
3.88	4.45	99.6	2	0.102	0.994
3.53	3.88	99.8	2	0.116	1.129
3.28	3.53	99.7	2	0.14	0.954
3.08	3.28	99	2	0.173	0.879
2.93	3.08	93	2	0.196	0.952
2.8	2.93	80.1	2	0.218	0.818
2.69	2.8	68.3	2	0.286	0.667
2.6	2.69	57.7	2	0.297	0.595

Reflection

Resolution: 2.6→50 Å / Num. all: 25548 / Num. obs: 23601 / % possible obs: 92.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / R_merge(I) obs: 0.078 / Net I/σ(I): 12.3

Reflection shell

Resolution: 2.6→2.69 Å / R_merge(I) obs: 0.204 / Mean I/σ(I) obs: 3.6 / % possible all: 64

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Phasing

Phasing

Method:

SAD

Phasing MAD

D res high: 3.1 Å / D res low: 30 Å / FOM : 0.35 / Reflection: 14223

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	7.493	20.535	65.714	SE	38.3	0.85
2	-6.116	49.511	61.534	SE	60	0.9
3	21.198	25.649	115.694	SE	60	0.84
4	32.057	26.735	95.125	SE	60	0.67
5	-8.584	43.929	61.592	SE	60	0.68
6	-2.542	22.219	95.134	SE	60	0.63
7	-11.49	23.167	111.092	SE	40.5	0.47
8	10.746	14.467	65.777	SE	60	0.39

Phasing MAD shell

Resolution (Å)	FOM	Reflection
11.5-30	0.35	624
7.42-11.5	0.4	1018
5.85-7.42	0.42	1259
4.98-5.85	0.38	1489
4.41-4.98	0.33	1652
3.99-4.41	0.3	1826
3.68-3.99	0.29	1957
3.43-3.68	0.27	2054

Phasing dm

FOM : 0.68 / FOM acentric: 0.68 / FOM centric: 0.57 / Reflection: 14224 / Reflection acentric: 13110 / Reflection centric: 1114

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
8.9-27.727	0.9	0.94	0.74	649	507	142
5.5-8.9	0.81	0.84	0.59	1972	1741	231
4.4-5.5	0.78	0.8	0.62	2444	2233	211
3.9-4.4	0.75	0.76	0.66	2413	2255	158
3.3-3.9	0.62	0.63	0.46	4239	3987	252
3.1-3.3	0.43	0.44	0.31	2507	2387	120

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SOLVE	2.1	phasing
RESOLVE	2.1	phasing
REFMAC		refinement
PDB_EXTRACT	2	data extraction
ADSC	QUANTUM	data collection
HKL-2000		data reduction

Refinement

Method to determine structure:

SAD / Resolution: 2.58→50 Å / Cor.coef. F_o:F_c: 0.931 / Cor.coef. F_o:F_c free: 0.864 / SU B: 26.361 / SU ML: 0.288 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 2.041 / ESU R Free: 0.404 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.30249	1137	4.8 %	RANDOM
R_work	0.22754	-	-	-
obs	0.23122	22455	91.02 %	-
all	-	24164	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 30.643 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.79 Å²	0 Å²	1.47 Å²
2-	-	0.45 Å²	0 Å²
3-	-	-	-3.67 Å²

Refinement step

Cycle: LAST / Resolution: 2.58→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5400	0	0	89	5489

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	5455
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.293	1.98	7363
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.188	5	683
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.19	25.867	271
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.043	15	1061
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.271	15	38
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	863
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	4056
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.233	0.2	2428
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.302	0.2	3824
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.16	0.2	208
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.177	0.2	69
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.221	0.2	10
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.493	1.5	3510
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.826	2	5516
X-RAY DIFFRACTION	r_scbond_it	1.297	3	2125
X-RAY DIFFRACTION	r_scangle_it	2.144	4.5	1847
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.578→2.645 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.413	52	-
R_work	0.27	817	-
obs	-	-	45.28 %

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	4.8777	0.8059	-6.6324	3.0347	-2.2617	15.4067	0.0107	-0.35	0.3238	0.2894	0.1926	0.1461	0.106	0.3665	-0.2033	0.0634	0.0314	-0.0252	0.1748	-0.0234	0.1269	-34.8738	30.6852	113.7119
2	0.8424	0.0445	0.0377	1.4598	-0.4021	2.5415	-0.0824	-0.0686	-0.0599	0.0767	0.0432	0.1177	-0.0297	-0.1555	0.0392	0.2005	-0.0098	0.0149	0.1373	0.0049	0.14	-23.3282	34.1135	77.9316
3	0.2983	-0.5478	-3.4129	3.4374	7.0785	39.3138	-0.1282	-0.0244	0.039	-0.4022	-0.5273	0.0097	-1.4819	-0.0648	0.6554	0.2596	0.0492	0.0166	0.1132	-0.0475	0.0609	-24.8542	55.1793	97.8322
4	0.1638	0.054	0.4772	2.363	2.9984	8.1185	-0.0635	-0.1485	0.1314	0.0403	-0.0551	-0.0422	-0.1654	-0.0743	0.1186	0.0682	0.0084	0.0114	0.1608	-0.0243	0.1367	-24.9884	56.2482	129.2599
5	3.6154	-0.364	-6.7697	0.4256	2.8512	24.7789	-0.4114	-0.2461	-0.023	-0.1316	0.0903	-0.0526	-0.1098	1.0328	0.3211	0.2946	0.042	0.1037	0.1168	-0.0159	0.0718	-15.8856	46.4301	93.0843
6	5.5982	0.5859	-0.3454	2.0847	-2.7365	3.6251	0.1795	0.4387	0.0386	-0.2244	-0.1484	0.0439	-0.0986	-0.1339	-0.0311	0.1816	-0.003	0.0278	0.1285	0.0187	0.1271	-17.7484	41.1181	68.114
7	9.3223	-4.2137	-12.3466	5.9453	6.4478	27.2335	-0.0763	0.6645	-0.2996	-0.3624	-0.1494	0.1542	-0.0979	-0.781	0.2257	0.1982	-0.0114	0.0176	0.1065	-0.0126	0.1224	-25.8608	20.7762	74.0699
8	7.6547	-4.2744	-9.4985	3.2867	4.5226	21.8929	0.0258	1.0806	-0.4578	-0.2614	-0.8311	-0.0564	-0.571	-2.1511	0.8054	0.1806	-0.0653	-0.0268	0.1457	-0.0383	0.0664	-38.5271	29.2772	97.1626
9	2.7864	-1.8156	-3.9878	13.4745	-0.5627	13.2904	-0.5907	0.7548	-0.4751	0.0245	0.018	0.0481	-0.4186	-0.0148	0.5727	0.0221	-0.0748	0.03	0.15	0.0092	0.1498	-47.2244	26.5069	120.5848
10	1.9678	-1.4184	-3.8573	1.6183	1.6517	9.6992	-0.7683	-0.5078	-0.5593	-0.0221	0.0649	0.084	0.9001	0.4034	0.7034	0.2065	0.0656	0.1568	0.1613	0.0479	0.1483	-38.6885	21.2668	112.5355
11	1.8445	-0.0527	-2.2619	4.4185	-0.0587	3.0866	-0.1932	-0.0657	-0.3729	0.0181	-0.083	-0.2168	0.2376	0.117	0.2763	0.1264	0.048	-0.0168	0.1168	0.0393	0.1286	-16.2356	25.418	77.0826
12	0.9847	-2.0556	-4.3912	4.2911	9.1667	19.5821	-0.4769	-0.1023	-0.2872	0.2343	-0.3464	0.4641	0.2498	-0.3778	0.8233	0.2572	0.0379	0.037	0.18	-0.0354	0.0532	-28.8171	46.1884	98.45
13	4.2648	-1.9937	-0.4483	4.6976	-1.2374	3.0409	-0.1183	-0.1729	-0.0279	0.3611	-0.3574	0.3743	-0.7629	-1.0745	0.4757	0.122	0.0575	0.0103	0.1971	-0.0686	0.1343	-35.0364	57.8949	126.9696
14	4.5607	-0.9173	-8.9036	0.3222	2.8834	26.0513	-0.0593	-0.214	-0.1091	-0.1143	0.1129	-0.0894	-0.0248	0.4178	-0.0536	0.1548	-0.0155	-0.0405	0.1548	0.0282	0.0972	-3.2786	26.2628	113.2756
15	2.5486	-0.6501	-0.6588	3.1432	-0.1565	7.1199	-0.0005	0.0431	-0.0181	-0.2391	-0.0231	-0.0643	-0.2172	-0.1094	0.0235	0.1812	-0.0193	-0.0055	0.1031	-0.0284	0.104	6.8013	27.562	76.832
16	4.1319	3.4136	3.7102	9.9928	12.8831	25.9048	-0.3311	-0.1243	0.3314	-1.4614	-0.093	0.2783	-1.7251	0.2485	0.4241	0.4076	0.1152	-0.0517	-0.0157	0.0075	-0.0137	4.8041	47.7114	87.3884
17	1.3739	0.7626	0.7079	3.8272	3.9714	7.3081	0.0551	-0.1077	0.137	-0.0199	-0.0129	-0.0534	-0.2892	0.4182	-0.0422	0.1304	0.0057	-0.0504	0.1377	-0.0045	0.1582	9.1819	57.9857	128.384
18	2.2509	-0.643	-5.2083	2.5052	4.7936	16.7584	-0.1898	0.0987	-0.0981	-0.4879	0.1099	-0.1437	-0.1248	0.9717	0.0799	0.1634	0.0374	-0.0065	0.1859	0.0023	0.089	11.766	44.8592	109.2945
19	0.7495	1.1326	0.9487	2.5996	0.8002	2.7655	0.0642	0.2418	0.0396	-0.3739	0.4075	-0.3197	-1.1247	0.2779	-0.4717	0.4443	-0.1206	0.2051	0.1223	-0.0471	0.039	11.4368	35.62	69.8358
20	4.0957	0.9653	-3.9419	0.5348	1.1658	18.0763	0.2425	0.0311	-0.3182	-0.7369	-0.4769	0.4535	-0.9822	-1.1379	0.2344	0.2118	0.0432	-0.0192	0.146	0.0045	0.1064	0.9297	16.8049	76.058
21	8.9809	-1.7001	-16.2784	2.3165	5.559	32.5827	0.2768	0.5787	0.1434	-0.3981	-0.2361	0.4099	-0.6976	-1.6447	-0.0406	0.0815	0.1236	-0.0948	0.25	0.0285	0.1054	-10.1837	26.0236	100.5915
22	2.5368	-1.1277	-3.8885	2.5336	0.6601	7.355	-0.1153	0.0144	-0.0898	0.1855	0.1153	0.3451	0.7532	-0.3029	0	0.0737	-0.0821	-0.0538	0.2106	-0.0086	0.1154	-9.5266	18.4235	114.0835
23	14.277	-1.2358	-14.777	4.2713	4.6733	27.0924	-0.0996	0.3963	-0.6311	0.1288	-0.0317	-0.5923	0.6276	0.6784	0.1312	0.124	0.0715	-0.0429	0.166	-0.0235	0.1014	9.3312	14.4996	79.018
24	2.4602	-1.1344	-2.3747	4.8772	4.551	7.6533	-0.3711	-0.0026	-0.1349	-0.1258	0.4112	-0.3857	-0.1666	0.6034	-0.0401	0.2168	-0.0508	-0.0375	0.1994	-0.0326	0.1326	11.202	34.2533	81.1016
25	1.8098	-1.4076	-1.8005	7.1963	5.9076	13.2098	-0.0105	-0.0022	-0.0732	-0.1061	-0.4696	0.5021	-0.2575	-0.5426	0.4801	0.122	0.0066	-0.0364	0.1589	0.0071	0.1714	-0.2726	54.5285	119.4475

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	A	A	361 - 383	10 - 32
2	2	A	A	384 - 430	33 - 79
3	3	A	A	431 - 449	80 - 98
4	4	A	A	450 - 500	99 - 149
5	5	A	A	501 - 519	150 - 168
6	6	A	A	520 - 541	169 - 190
7	7	A	A	542 - 563	191 - 212
8	8	A	A	564 - 578	213 - 227
9	9	A	A	579 - 589	228 - 238
10	10	A	A	590 - 616	239 - 265
11	11	A	A	617 - 660	266 - 309
12	12	A	A	661 - 685	310 - 334
13	13	A	A	686 - 702	335 - 351
14	14	B	B	362 - 384	11 - 33
15	15	B	B	385 - 421	34 - 70
16	16	B	B	422 - 443	71 - 92
17	17	B	B	444 - 484	93 - 133
18	18	B	B	485 - 514	134 - 163
19	19	B	B	515 - 545	164 - 194
20	20	B	B	546 - 563	195 - 212
21	21	B	B	564 - 582	213 - 231
22	22	B	B	583 - 617	232 - 266
23	23	B	B	618 - 641	267 - 290
24	24	B	B	642 - 675	291 - 324
25	25	B	B	676 - 702	325 - 351

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