PDB-3ssu: Crystal structure of vimentin coil1A/1B fragment

ID or keywords:

Entry

Database: PDB / ID: 3ssu

Title

Crystal structure of vimentin coil1A/1B fragment

Components

Vimentin

Keywords

STRUCTURAL PROTEIN / cytoskeleton / intermediate filament / alpha-helix

Function / homology

Function and homology information

lens fiber cell development / keratin filament binding / intermediate filament organization / cellular response to muramyl dipeptide / structural constituent of eye lens / astrocyte development / Striated Muscle Contraction / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton / microtubule organizing center ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.603 Å

Authors

Nicolet, S. / Chernyatina, A.A. / Strelkov, S.V.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Atomic structure of the vimentin central alpha-helical domain and its implications for intermediate filament assembly.
Authors: Chernyatina, A.A. / Nicolet, S. / Aebi, U. / Herrmann, H. / Strelkov, S.V.

History

Deposition	Jul 8, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 15, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jul 3, 2013	Group: Database references
Revision 1.2	Feb 28, 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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PDBx/mmCIF format	3ssu.cif.gz	51.4 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3ssu_validation.pdf.gz	427.6 KB	Display	wwPDB validaton report
Full document	3ssu_full_validation.pdf.gz	428.3 KB	Display
Data in XML	3ssu_validation.xml.gz	5 KB	Display
Data in CIF	3ssu_validation.cif.gz	5.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ss/3ssu ftp://data.pdbj.org/pub/pdb/validation_reports/ss/3ssu	HTTPS FTP

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Related structure data

Related structure data	3s4rC 3swkC C: citing same article (ref.)
Similar structure data	1g1j-d 1g1i-d 5f9i-1 3a2a-2 3q69-d 3r62-1 5eqz-d 5a17-d 5x9x-d 3a2a-1 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	#185 - May 2015 Titin similarity (1) #152 - Aug 2012 cAMP-dependent Protein Kinase similarity (1) #56 - Aug 2004 Caspases similarity (1) #19 - Jul 2001 Actin similarity (1)

Deposited unit

A: Vimentin

B: Vimentin

22.3 kDa, 2 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)	45.600, 83.497, 118.606
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	24
Space group name H-M	I2₁2₁2₁

#1: Protein	Vimentin Mass: 11138.536 Da / Num. of mol.: 2 / Fragment: UNP residues 99-189 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FLJ36605, VIM / Plasmid: pPEP-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P08670

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal

ID	Density Matthews (Å³/Da)	Density % sol (%)
1	2.55	51.68
2

Crystal grow

Temperature (K)	Crystal-ID	Method	pH	Details
277	1	vapor diffusion, hanging drop	6	0.04M calcium acetate, 0.1M MES pH 6, isopropanol 6%, VAPOR DIFFUSION, HANGING DROP, temperature 277K
277	2	vapor diffusion, hanging drop	5.5	0.06M calcium acetate, 0.1M MES pH 5.5, isopropanol 6%, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1
3	100	1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	SLS	X06DA	1	0.9786
SYNCHROTRON	SLS	X06DA	2	0.9392
SYNCHROTRON	SLS	X06DA	3	0.97625

Detector

Type	ID	Detector	Date
MARMOSAIC 225 mm CCD	1	CCD	Jul 5, 2005
MARMOSAIC 225 mm CCD	2	CCD	Jul 5, 2005
MARMOSAIC 225 mm CCD	3	CCD	Apr 25, 2005

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Bartels Monochromator	SINGLE WAVELENGTH	M	x-ray	1
2	Bartels Monochromator	SINGLE WAVELENGTH	M	x-ray	1
3	Bartels Monochromator	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9786	1
2	0.9392	1
3	0.97625	1

Reflection

Redundancy: 12.8 % / Av σ(I) over netI: 25.15 / Number: 60764 / R_merge(I) obs: 0.096 / Χ²: 2.22 / D res high: 3 Å / D res low: 50 Å / Num. obs: 4745 / % possible obs: 99.6

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
8.13	50	96.4	1	0.054	4.146	9
6.46	8.13	100	1	0.066	3.897	10.9
5.64	6.46	100	1	0.1	3.349	11.8
5.13	5.64	100	1	0.102	3.282	12.4
4.76	5.13	100	1	0.08	3.364	12.4
4.48	4.76	100	1	0.079	3.077	13
4.26	4.48	100	1	0.087	3.027	13.3
4.07	4.26	100	1	0.085	2.552	13.4
3.91	4.07	100	1	0.082	2.228	13.8
3.78	3.91	100	1	0.093	2.176	13.9
3.66	3.78	100	1	0.098	2.065	13.9
3.56	3.66	100	1	0.131	1.612	13.9
3.46	3.56	100	1	0.14	1.608	14.2
3.38	3.46	100	1	0.194	1.513	13.9
3.3	3.38	100	1	0.233	1.28	13.9
3.23	3.3	100	1	0.278	1.201	13.6
3.17	3.23	100	1	0.253	1.211	13.2
3.11	3.17	100	1	0.322	1.199	12.7
3.05	3.11	98.7	1	0.306	1.11	12.4
3	3.05	97.9	1	0.277	1.151	11.1

Reflection

Resolution: 2.6→30 Å / Num. all: 7261 / Num. obs: 7261 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / R_sym value: 0.072 / Χ²: 1.03 / Net I/σ(I): 8.9

Reflection shell

Resolution (Å)	Redundancy (%)	Num. unique all	R_sym value	Χ²	Diffraction-ID	% possible all
2.6-2.64	5.6	358	0.599	0.735	1,2,3	100
2.64-2.69	5.5	371	0.643	0.828	1,2,3	100
2.69-2.74	5.7	338	0.496	0.664	1,2,3	100
2.74-2.8	5.6	361	0.374	0.71	1,2,3	100
2.8-2.86	5.6	352	0.303	0.879	1,2,3	100
2.86-2.93	5.6	358	0.282	0.799	1,2,3	100
2.93-3	5.6	348	0.199	0.792	1,2,3	100
3-3.08	5.6	355	0.186	0.852	1,2,3	100
3.08-3.17	5.6	368	0.157	0.771	1,2,3	100
3.17-3.28	5.6	354	0.135	0.822	1,2,3	100
3.28-3.39	5.6	356	0.117	0.79	1,2,3	100
3.39-3.53	5.6	367	0.091	0.943	1,2,3	100
3.53-3.69	5.5	355	0.162	2.269	1,2,3	100
3.69-3.88	5.5	361	0.05	1.054	1,2,3	100
3.88-4.12	5.5	368	0.047	1.154	1,2,3	100
4.12-4.44	5.4	361	0.051	1.387	1,2,3	100
4.44-4.89	5.4	369	0.052	1.768	1,2,3	100
4.89-5.59	5.4	380	0.055	1.655	1,2,3	100
5.59-7.03	5.3	379	0.039	0.962	1,2,3	100
7.03-30	4.8	402	0.016	0.761	1,2,3	98

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Phasing

Phasing

Method:

SAD

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 4707

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
6.49-100	78.7	0.508	501
5.12-6.49	74.1	0.559	501
4.46-5.12	71.5	0.542	502
4.04-4.46	67.8	0.532	501
3.74-4.04	73.2	0.538	501
3.51-3.74	69.3	0.486	502
3.33-3.51	91.2	0.443	506
3.18-3.33	89.9	0.423	504
3.01-3.18	95.6	0.367	689

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHELX		phasing
DM		phasing
PHENIX	1.6.4_486	refinement
PDB_EXTRACT	3.1	data extraction
GO.COM		data collection
SHELXD		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.603→24.293 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.32 / σ(F): 0 / Phase error: 31.62 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2719	722	9.97 %
R_work	0.2369	-	-
obs	0.2403	7244	99.74 %

Solvent computation

Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 43.365 Å² / k_sol: 0.324 e/Å³

Displacement parameters

B_iso max: 228.09 Å² / B_iso mean: 93.7573 Å² / B_iso min: 32.64 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-14.238 Å²	0 Å²	0 Å²
2-	-	30.5024 Å²	0 Å²
3-	-	-	-16.2644 Å²

Refinement step

Cycle: LAST / Resolution: 2.603→24.293 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	730	0	0	0	730

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	730
X-RAY DIFFRACTION	f_angle_d	1.097	971
X-RAY DIFFRACTION	f_chiral_restr	0.062	106
X-RAY DIFFRACTION	f_plane_restr	0.003	133
X-RAY DIFFRACTION	f_dihedral_angle_d	14.766	311

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all
2.603-2.8037	0.3942	141	0.3486	1281	1422
2.8037-3.0854	0.2783	141	0.2535	1265	1406
3.0854-3.5306	0.2924	143	0.2588	1299	1442
3.5306-4.4438	0.224	144	0.2003	1301	1445
4.4438-24.2944	0.2776	153	0.2305	1376	1529

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	9.6474	3.0969	7.1683	8.2594	3.9212	2.0045	-0.5853	-0.7988	0.0151	-0.943	-0.0563	-1.0813	0.1193	-1.153	0.6933	0.916	0.0999	0.0564	0.8958	-0.6696	0.7693	1.6542	4.7815	28.7714
2	2.6173	1.4098	1.915	3.1219	0.7159	1.0783	-0.1988	0.5716	-0.14	0.1925	0.3605	-0.0313	-0.0846	0.6203	-0.1723	0.2573	-0.0008	0.0087	0.3703	0.029	0.2299	-1.607	-8.2632	8.8843
3	-0.0103	-0.0994	0.0799	0.4698	0.0633	0.6895	0.2728	2.1419	-0.732	0.029	-0.0535	-0.6583	0.113	1.1631	-0.2003	0.173	0.0271	0.0117	0.9046	-0.1903	0.4279	-6.3381	-24.3759	-11.9603
4	2.7687	-0.9617	0.5886	2.5316	0.384	1.1163	-0.7176	0.1073	0.1609	0.2941	1.2437	0.1511	-0.5271	0.8266	-0.5103	0.8688	0.3092	0.1172	1.1525	-0.1627	0.7911	-10.293	1.6701	22.5953
5	0.55	-1.5209	-0.4621	4.4283	3.1122	3.8506	0.3604	-0.2867	-0.1649	0.1633	-0.616	0.2584	0.0268	-1.2373	0.2591	0.2763	-0.0119	-0.0153	0.5252	-0.0704	0.3111	-8.1778	-16.1984	8.7058
6	6.4846	-2.9949	4.8536	7.3416	-6.0879	6.176	-0.2064	-1.6466	-1.7546	-1.1016	0.1342	2.18	0.0126	-0.9539	0.4255	0.2279	-0.0313	-0.0655	0.4828	-0.3892	0.7529	-4.6852	-32.7508	-3.7825

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain A and resid 144:154)	A	144 - 154
2	X-RAY DIFFRACTION	2	(chain A and resid 155:176)	A	155 - 176
3	X-RAY DIFFRACTION	3	(chain A and resid 177:189)	A	177 - 189
4	X-RAY DIFFRACTION	4	(chain B and resid 147:159)	B	147 - 159
5	X-RAY DIFFRACTION	5	(chain B and resid 160:179)	B	160 - 179
6	X-RAY DIFFRACTION	6	(chain B and resid 180:187)	B	180 - 187

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