PDB-3umn: Crystal Structure of Lamin-B1

ID or keywords:

Entry

Database: PDB / ID: 3umn

Title

Crystal Structure of Lamin-B1

Components

Lamin-B1

Keywords

STRUCTURAL PROTEIN / Structural Genomics Consortium / SGC / Ig-like domain / INTERMEDIATE FILAMENT / LIPOPROTEIN / MEMBRANE / NUCLEUS

Function / homology

Function and homology information

structural constituent of nuclear lamina / Breakdown of the nuclear lamina / Depolymerization of the Nuclear Lamina / Nuclear Envelope Breakdown / nuclear envelope organization / nuclear pore localization / lamin filament / protein localization to nuclear envelope / nuclear lamina / Initiation of Nuclear Envelope (NE) Reformation ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Xu, C. / Bian, C.B. / Amaya, M.F. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Structural Genomics Consortium (SGC)

Citation

Journal: Febs Lett. / Year: 2012
Title: Crystal structures of the coil 2B fragment and the globular tail domain of human lamin B1.
Authors: Ruan, J. / Xu, C. / Bian, C. / Lam, R. / Wang, J.P. / Kania, J. / Min, J. / Zang, J.

History

Deposition	Nov 14, 2011	Deposition site: RCSB / Processing site: RCSB
Supersession	Nov 30, 2011	ID: 3HN9
Revision 1.0	Nov 30, 2011	Provider: repository / Type: Initial release
Revision 1.1	Mar 7, 2012	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3umn.cif.gz	146.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3umn.ent.gz	118.5 KB	Display	PDB format
PDBx/mmJSON format	3umn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3umn_validation.pdf.gz	440.6 KB	Display	wwPDB validaton report
Full document	3umn_full_validation.pdf.gz	445.4 KB	Display
Data in XML	3umn_validation.xml.gz	15.8 KB	Display
Data in CIF	3umn_validation.cif.gz	21.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/um/3umn ftp://data.pdbj.org/pub/pdb/validation_reports/um/3umn	HTTPS FTP

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Related structure data

Related structure data	3tyyC C: citing same article (ref.)
Similar structure data	2m8d-d 3jt0-2 3p0c-2 2lsj-d 4max-2 1ufi-2 4ijl-d 5ju7-d 3d1p-d 5lmj-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

3tyyC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#213 - Sep 2017 Sirtuins similarity (2) #79 - Jul 2006 Amyloid-beta Precursor Protein similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #189 - Sep 2015 Amyloids similarity (1) #85 - Jan 2007 Importins similarity (1) #122 - Feb 2010 Enhanceosome similarity (2) #94 - Oct 2007 Superoxide Dismutase similarity (2) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #47 - Nov 2003 Simian Virus 40 similarity (1) #128 - Aug 2010 Interferons similarity (1) #163 - Jul 2013 HIV Capsid similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

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NCBI

Related items in Molecule of the Month

#213 - Sep 2017
Sirtuins
similarity (2)
#79 - Jul 2006
Amyloid-beta Precursor Protein
similarity (1)
#31 - Jul 2002
p53 Tumor Suppressor
similarity (1)
#189 - Sep 2015
Amyloids
similarity (1)
#85 - Jan 2007
Importins
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (2)
#94 - Oct 2007
Superoxide Dismutase
similarity (2)
#221 - May 2018
Human Papillomavirus and Vaccines
similarity (1)
#234 - Jun 2019
MDM2 and Cancer
similarity (1)
#47 - Nov 2003
Simian Virus 40
similarity (1)
#128 - Aug 2010
Interferons
similarity (1)
#163 - Jul 2013
HIV Capsid
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: Lamin-B1

B: Lamin-B1

C: Lamin-B1

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

1

A: Lamin-B1

defined by author&software
13.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Lamin-B1

defined by author&software
13.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Lamin-B1

defined by author&software
13.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	107.538, 169.963, 53.613
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	21
Space group name H-M	C222

Components on special symmetry positions

ID	Model	Components
1	1	A-1- HOH

#1: Protein	Lamin-B1 Mass: 13426.978 Da / Num. of mol.: 3 / Fragment: Globular Tail Domain, UNP residues 428-550 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LMNB1, LMN2, LMNB / Production host: Escherichia coli (E. coli) / References: UniProt: P20700
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 104 / 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: 3.04 Å³/Da / Density % sol: 59.55 %
Crystal grow	Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 300.0K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54178 Å
Detector	Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: May 28, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54178 Å / Relative weight: 1
Reflection	Resolution: 2→100 Å / Num. all: 33777 / Num. obs: 33473 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
REFMAC	5.6.0117	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→25.06 Å / Cor.coef. F_o:F_c: 0.942 / Cor.coef. F_o:F_c free: 0.928 / SU B: 9.533 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26397	1698	5.1 %	RANDOM
R_work	0.24264	-	-	-
obs	0.24374	31763	99.34 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 66.645 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.06 Å²	-0 Å²	0 Å²
2-	-	-0 Å²	0 Å²
3-	-	-	0.07 Å²

Refinement step

Cycle: LAST / Resolution: 2→25.06 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2711	0	0	104	2815

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.034	0.02	2759
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.424	1.926	3738
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.703	5	349
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.698	25.385	117
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.333	15	484
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.956	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.151	0.2	423
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	2044
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2→2.052 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.337	114	-
R_work	0.388	2001	-
obs	-	-	92.6 %

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	0.8428	-0.1656	0.0378	0.2331	0.1574	0.1418	0.0021	0.0418	0.0452	-0.0103	-0.0686	0.0906	0.0165	-0.0298	0.0665	0.1425	-0.0139	-0.017	0.1476	-0.0121	0.1186	5.6344	40.2457	30.0713
2	0.1875	0.3171	0.2174	0.8172	0.4878	0.3038	-0.0186	-0.0009	0.0313	0.0284	0.0401	-0.0619	0.0099	0.0199	-0.0215	0.1352	-0.0121	-0.0098	0.1404	-0.0003	0.1153	16.3071	42.402	35.9552
3	0.2716	0.0921	-0.1972	0.2476	0.2147	0.5364	0.0354	0.0325	-0.0219	0.0543	-0.0137	-0.0106	0.0622	-0.0321	-0.0217	0.1773	-0.0194	-0.006	0.1193	0.0024	0.0849	12.0185	32.7541	38.1691
4	2.0593	0.1728	0.3935	0.0158	0.0384	0.2436	-0.0101	-0.0456	0.2678	-0.0046	-0.0024	0.0109	0.0545	-0.0542	0.0125	0.136	-0.0008	0.0021	0.13	-0.0034	0.1546	13.1457	47.947	33.4441
5	10.1157	-1.8599	-2.2182	1.3016	2.0315	3.2421	0.1065	-0.2665	0.3285	-0.1328	-0.2504	0.0764	-0.2122	-0.3609	0.1439	0.096	0.0072	-0.0481	0.2182	-0.0293	0.16	-1.2311	49.3125	34.7096
6	1.4087	-2.0587	-2.5586	16.9095	18.8194	21.0082	0.1778	0.0098	-0.0425	-0.1657	-0.0237	-0.1702	-0.2216	-0.0543	-0.1541	0.1687	0.0002	0.0424	0.08	-0.0195	0.0933	19.1291	21.0514	50.8885
7	0.3657	0.3194	0.2247	0.2893	0.2603	0.8115	0.0278	-0.0279	-0.0082	-0.0028	-0.0308	-0.0114	-0.0357	0.0182	0.0029	0.1543	-0.0026	0.0082	0.1168	-0.0183	0.1256	18.8104	17.4938	62.1511
8	0.8558	0.1804	0.7814	0.6062	1.2152	2.6596	0.1591	-0.1066	-0.0542	-0.1034	0.0029	-0.0718	-0.1083	-0.0797	-0.162	0.149	-0.0249	0.0033	0.1313	0.0108	0.1134	5.9467	16.1484	58.7251
9	0.0283	-0.0477	-0.0021	0.6547	0.032	0.0074	0.0445	-0.0362	-0.0262	0.1451	-0.0665	-0.0747	0.0339	0.0034	0.0219	0.2226	-0.044	-0.0203	0.1644	0.0207	0.1239	15.094	13.6056	68.4757
10	1.6189	0.4873	1.29	2.5256	0.3973	1.032	-0.0167	-0.0205	0.0061	0.2315	0.0213	0.1012	-0.0083	-0.0375	-0.0046	0.1668	-0.0195	0.0103	0.1264	0.0117	0.0591	11.4064	6.2823	66.1772
11	1.202	-0.5679	-1.5429	0.2693	0.7298	1.9824	0.0561	0.0254	0.0279	-0.0319	-0.0157	-0.0217	-0.0781	-0.0465	-0.0404	0.1728	-0.0065	-0.0094	0.1267	-0.0009	0.1031	10.7294	13.8705	51.8388
12	4.7871	-1.5755	0.6855	6.7074	-0.7652	4.0662	-0.0026	0.0514	0.5317	0.1554	-0.0547	-0.1638	-0.2561	-0.224	0.0573	0.1399	0.0057	0.0166	0.0824	-0.0242	0.0869	7.7927	28.2718	61.8874
13	1.1201	1.2221	0.8822	1.6405	1.8818	3.4803	0.0832	0.1048	-0.015	0.1121	0.0849	-0.0913	0.1721	-0.0862	-0.1681	0.1607	0.0042	0.0091	0.1222	-0.0224	0.1219	16.0971	16.4193	47.3223
14	0.8068	0.7194	-0.3764	0.642	-0.3353	0.1776	-0.0295	-0.049	-0.1512	-0.0294	-0.05	-0.1382	0.0041	0.0156	0.0795	0.1289	-0.0031	0.0297	0.124	-0.0133	0.15	29.3488	20.2491	54.517
15	1.2051	0.3986	-1.1545	3.4888	-0.5024	1.1121	0.0105	0.0582	-0.2681	-0.0002	-0.269	-0.0226	-0.0173	-0.0359	0.2585	0.0821	-0.0121	0.0553	0.1314	0.008	0.1783	37.3658	25.6479	46.8368
16	2.4684	-0.3633	0.459	0.0706	-0.0693	0.0856	0.0046	-0.1306	-0.3437	-0.0081	0.0215	-0.0296	-0.004	-0.0213	-0.0262	0.0184	0.0173	0.0646	0.0521	0.1454	0.427	40.453	16.3031	52.5684
17	0.8877	-0.2627	-0.7568	0.1837	0.1841	0.6602	0.1338	-0.0914	-0.029	-0.0038	-0.1518	-0.0136	-0.1468	0.1381	0.018	0.0465	-0.0796	-0.0393	0.2499	0.0451	0.1787	41.7593	25.9881	58.5453
18	0.8674	-0.4067	-1.0067	2.2897	1.9514	2.2215	-0.004	0.1054	-0.1627	0.0531	-0.0995	-0.0517	0.0079	-0.1388	0.1034	0.151	-0.0399	0.0403	0.1508	-0.03	0.1268	29.6636	26.6216	47.3987

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	431 - 461
2	X-RAY DIFFRACTION	2	A	462 - 486
3	X-RAY DIFFRACTION	3	A	487 - 523
4	X-RAY DIFFRACTION	4	A	524 - 540
5	X-RAY DIFFRACTION	5	A	541 - 548
6	X-RAY DIFFRACTION	6	B	432 - 440
7	X-RAY DIFFRACTION	7	B	441 - 466
8	X-RAY DIFFRACTION	8	B	467 - 484
9	X-RAY DIFFRACTION	9	B	485 - 503
10	X-RAY DIFFRACTION	10	B	504 - 520
11	X-RAY DIFFRACTION	11	B	521 - 532
12	X-RAY DIFFRACTION	12	B	533 - 539
13	X-RAY DIFFRACTION	13	B	540 - 547
14	X-RAY DIFFRACTION	14	C	431 - 463
15	X-RAY DIFFRACTION	15	C	464 - 480
16	X-RAY DIFFRACTION	16	C	481 - 501
17	X-RAY DIFFRACTION	17	C	502 - 526
18	X-RAY DIFFRACTION	18	C	527 - 548

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