PDB-7yvd: The crystal structure of the progerin C-terminal peptide and the ...

ID or keywords:

Entry

Database: PDB / ID: 7yvd

Title

The crystal structure of the progerin C-terminal peptide and the Ig-like domain of lamin A/C

Components

Lamin-A/C

Keywords

NUCLEAR PROTEIN / nuclear lamin / progerin / premature aging / HGPS / laminopathies

Function / homology

Function and homology information

structural constituent of nuclear lamina / negative regulation of mesenchymal cell proliferation / establishment or maintenance of microtubule cytoskeleton polarity / ventricular cardiac muscle cell development / Breakdown of the nuclear lamina / DNA double-strand break attachment to nuclear envelope / Depolymerization of the Nuclear Lamina / Nuclear Envelope Breakdown / nuclear envelope organization / nuclear pore localization ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Ahn, J. / Ha, N.C.

Funding support

Korea, Republic Of, 2items

Citation

Journal: To Be Published
Title: The crystal structure of the progerin C-terminal peptide and the Ig-like domain of lamin A/C
Authors: Ahn, J. / Ha, N.C.

History

Deposition	Aug 19, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 30, 2023	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7yvd.cif.gz	178.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7yvd.ent.gz	141.2 KB	Display	PDB format
PDBx/mmJSON format	7yvd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7yvd_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	7yvd_full_validation.pdf.gz	1 MB	Display
Data in XML	7yvd_validation.xml.gz	20.8 KB	Display
Data in CIF	7yvd_validation.cif.gz	29.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yv/7yvd ftp://data.pdbj.org/pub/pdb/validation_reports/yv/7yvd	HTTPS FTP

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Related structure data

Related structure data	7crgS S: Starting model for refinement
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
Related items in Molecule of the Month	#213 - Sep 2017 Sirtuins similarity (1) #79 - Jul 2006 Amyloid-beta Precursor Protein similarity (1) #189 - Sep 2015 Amyloids similarity (1) #85 - Jan 2007 Importins similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #94 - Oct 2007 Superoxide Dismutase similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

Deposited unit

A: Lamin-A/C

B: Lamin-A/C

C: Lamin-A/C

hetero molecules

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

1

A: Lamin-A/C

hetero molecules

defined by author
Evidence: cross-linking, modified cysteine (SPQNC peptide linked)
14.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Lamin-A/C

hetero molecules

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

3

C: Lamin-A/C

hetero molecules

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

Unit cell

Length a, b, c (Å)	91.974, 91.974, 204.562
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	181
Space group name H-M	P6₄22

#1: Protein	Lamin-A/C / 70 kDa lamin / Renal carcinoma antigen NY-REN-32 Mass: 14747.106 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LMNA, LMN1 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P02545
#2: Chemical	ChemComp-SEC / SELENOCYSTEINE Type: L-peptide linking / Mass: 168.053 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₇NO₂Se / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.82 Å³/Da / Density % sol: 56.62 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion / pH: 6.5 Details: 0.1 M BIS-TRIS pH 6.5, 25% (v/v) Polyethylene glycol 300

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site: PAL/PLS

/ Beamline: 5C (4A) / Wavelength: 0.97926 Å

Detector

Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 14, 2021

Radiation

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

Radiation wavelength

Wavelength: 0.97926 Å / Relative weight: 1

Reflection

Resolution: 2.1→50 Å / Num. obs: 56656 / % possible obs: 99.7 % / Redundancy: 28.7 % / B_iso Wilson estimate: 23.34 Å² / R_merge(I) obs: 0.063 / R_pim(I) all: 0.011 / R_rim(I) all: 0.064 / Χ²: 1.062 / Net I/σ(I): 16.9

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.1-2.14	22.5	0.213	1487	0.993	0.044	0.218	0.98	99.7
2.14-2.18	23.6	0.197	1489	0.99	0.04	0.201	1.049	99.5
2.18-2.22	23.6	0.179	1505	0.995	0.036	0.183	1.031	99.7
2.22-2.26	23.8	0.178	1486	0.997	0.036	0.181	1.058	99.7
2.26-2.31	22.3	0.169	1533	0.997	0.035	0.173	1.025	99.7
2.31-2.37	22.4	0.158	1498	0.995	0.033	0.162	1.029	99.9
2.37-2.42	24.4	0.144	1526	0.997	0.029	0.147	1.022	99.9
2.42-2.49	25	0.134	1512	0.998	0.026	0.137	1.017	99.8
2.49-2.56	28.2	0.125	1511	0.998	0.023	0.128	0.992	99.8
2.56-2.65	29.8	0.106	1519	0.999	0.019	0.108	1.015	99.9
2.65-2.74	30.6	0.094	1521	0.999	0.017	0.096	1.043	99.7
2.74-2.85	30.6	0.087	1531	0.999	0.015	0.088	1.023	99.8
2.85-2.98	31.7	0.073	1531	1	0.013	0.075	1.057	99.8
2.98-3.14	32.1	0.065	1527	1	0.011	0.066	1.08	99.8
3.14-3.33	33.4	0.057	1554	1	0.01	0.058	1.166	99.8
3.33-3.59	34.1	0.049	1549	1	0.008	0.05	1.224	99.8
3.59-3.95	33.1	0.043	1569	1	0.007	0.043	1.219	99.7
3.95-4.52	29.9	0.036	1583	1	0.006	0.037	1.114	99.8
4.52-5.7	34.7	0.033	1625	1	0.006	0.034	1.027	99.6
5.7-50	35.1	0.032	1749	1	0.005	0.033	0.969	98.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PDB_EXTRACT	3.27	data extraction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7CRG

7crg

Resolution: 2.1→34.39 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.55 / Phase error: 18.14 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1954	3691	6.51 %
R_work	0.1638	-	-
obs	0.1659	56656	99.81 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.1→34.39 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3055	0	21	394	3470

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_dihedral_angle_d	4.885	435
X-RAY DIFFRACTION	f_chiral_restr	0.043	473
X-RAY DIFFRACTION	f_plane_restr	0.003	569

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 (%)
2.1-2.12	0.2349	133	0.1803	1979	X-RAY DIFFRACTION	98
2.12-2.15	0.2691	142	0.1744	2046	X-RAY DIFFRACTION	100
2.15-2.18	0.201	145	0.1581	2019	X-RAY DIFFRACTION	100
2.18-2.22	0.2016	144	0.1634	2047	X-RAY DIFFRACTION	100
2.22-2.25	0.2008	141	0.1638	2047	X-RAY DIFFRACTION	100
2.25-2.29	0.2239	142	0.1735	2022	X-RAY DIFFRACTION	100
2.29-2.33	0.2217	139	0.1701	2012	X-RAY DIFFRACTION	100
2.33-2.37	0.2081	141	0.1712	2065	X-RAY DIFFRACTION	100
2.37-2.42	0.1905	140	0.1676	2043	X-RAY DIFFRACTION	100
2.42-2.46	0.2176	145	0.172	2028	X-RAY DIFFRACTION	100
2.46-2.52	0.2286	141	0.1799	2043	X-RAY DIFFRACTION	100
2.52-2.58	0.1848	140	0.1752	2035	X-RAY DIFFRACTION	100
2.58-2.64	0.2082	142	0.1746	2050	X-RAY DIFFRACTION	100
2.64-2.71	0.2625	143	0.1731	2022	X-RAY DIFFRACTION	100
2.71-2.79	0.1811	144	0.1764	2065	X-RAY DIFFRACTION	100
2.79-2.88	0.2246	142	0.186	2036	X-RAY DIFFRACTION	100
2.88-2.99	0.2067	145	0.1802	2017	X-RAY DIFFRACTION	100
2.99-3.11	0.272	141	0.1808	2033	X-RAY DIFFRACTION	100
3.11-3.25	0.2084	146	0.1741	2067	X-RAY DIFFRACTION	100
3.25-3.42	0.1805	142	0.1624	2036	X-RAY DIFFRACTION	100
3.42-3.63	0.1707	137	0.1502	2049	X-RAY DIFFRACTION	100
3.63-3.91	0.1962	141	0.1445	2022	X-RAY DIFFRACTION	100
3.91-4.3	0.1547	148	0.137	2057	X-RAY DIFFRACTION	100
4.3-4.93	0.1348	140	0.1262	2034	X-RAY DIFFRACTION	100
4.93-6.2	0.1709	141	0.1608	2046	X-RAY DIFFRACTION	100
6.2-34.39	0.1901	146	0.1952	2045	X-RAY DIFFRACTION	100

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	4.7477	0.455	-0.7733	3.2943	1.6483	3.0594	0.0305	-0.1446	0.0843	0.2589	0.0027	-0.044	0.2675	-0.0169	-0.0195	0.1613	-0.0025	-0.0175	0.1135	-0.0198	0.0981	2.3909	35.4465	-16.6581
2	2.9957	-1.2899	-0.0869	4.8272	1.7866	3.1511	0.1564	0.0757	0.3548	-0.4547	-0.2731	0.3428	-0.4618	-0.2986	0.0716	0.1451	-0.0087	0.0082	0.2054	0.0106	0.2475	-4.4271	40.7481	-20.79
3	3.3413	-0.8318	0.0068	2.9287	2.2234	2.8647	0.1568	0.0408	0.0158	0.018	-0.4187	0.5215	-0.0749	-0.5384	0.2589	0.145	-0.0167	0.0327	0.1789	-0.0158	0.1863	-7.1325	35.5327	-21.1535
4	0.8944	0.8624	-0.0372	2.4972	0.858	2.0439	0.08	-0.0309	-0.1684	0.6289	-0.2545	0.2493	0.2448	-0.3325	0.1413	0.262	-0.0694	0.0643	0.1647	-0.0528	0.201	-4.6741	28.6534	-17.4508
5	4.027	-4.4559	-0.1627	5.286	-0.278	0.594	0.3739	0.4707	-0.1084	-0.4209	-0.369	0.0316	0.0662	0.0246	0.0795	0.2315	0.0157	-0.0177	0.1994	-0.0265	0.2333	9.6677	30.3253	-25.932
6	5.4869	-6.2827	2.6604	8.8609	-4.0814	3.0833	0.0034	-0.1701	0.1687	0.1399	0.0634	0.0169	-0.2299	-0.0732	-0.1027	0.164	-0.0514	0.0002	0.1567	-0.0166	0.2215	15.8861	37.6671	-20.7696
7	1.2987	0.5065	0.319	4.0976	-1.0119	2.3225	0.0752	-0.06	-0.1678	0.065	-0.1241	-0.1992	0.267	0.1523	0.0325	0.158	0.0031	-0.0315	0.1295	0.0185	0.1642	32.0893	17.8429	-5.4531
8	0.9306	-0.251	0.4609	2.1446	-1.4861	2.5179	-0.0215	-0.012	0.0254	0.2119	-0.0966	-0.1087	-0.1857	0.1272	0.1162	0.1432	-0.0295	-0.0148	0.0946	0.0018	0.1489	30.1529	25.9394	-6.0695
9	4.6778	-3.4908	-0.5031	6.807	-1.0241	2.2624	-0.0028	-0.0068	0.3109	0.2983	-0.1982	0.1658	-0.2961	-0.1089	0.1841	0.199	0.0023	-0.0633	0.1558	-0.0868	0.169	15.8687	17.8894	-33.1955
10	6.3608	-3.8181	-0.8789	4.7749	0.193	4.3128	0.2278	0.0836	0.0547	-0.2567	-0.2226	-0.0425	0.2592	0.3072	-0.0417	0.174	0.0074	-0.0082	0.0885	0.023	0.092	23.2165	-6.7871	-27.2941
11	4.1344	-1.6326	-1.3627	4.3287	1.4988	5.9454	0.0381	0.3551	-0.1298	0.2512	-0.3809	0.7236	-0.1113	-0.5212	0.3038	0.1801	-0.026	-0.0067	0.1468	-0.0263	0.1846	13.0647	-3.6869	-24.0058
12	1.9097	-0.7067	0.3863	4.8576	-0.3271	3.0396	-0.0292	-0.0703	-0.159	-0.0047	0.0772	-0.5337	0.2132	0.284	-0.086	0.1701	-0.0139	0.0207	0.1568	0.0406	0.1505	23.2768	-11.0378	-20.0422
13	1.3793	0.5056	0.0043	3.8667	0.0662	2.0719	0.1298	-0.0771	-0.0101	0.4119	-0.1409	0.1982	0.0007	-0.2344	0.0353	0.2036	-0.0321	0.0078	0.1399	0.001	0.1164	15.3798	-5.7811	-16.4684
14	2.9493	-4.1771	1.1895	6.4842	-1.9155	4.8309	-0.2231	0.0466	0.5278	0.3543	-0.2973	-1.0927	-0.349	0.7963	0.495	0.2129	-0.0401	-0.0901	0.2361	0.0598	0.2933	28.6892	-6.2529	-20.5561
15	4.0645	-2.6732	0.1738	8.7183	-2.4342	2.2676	-0.1115	-0.1183	0.2964	0.6088	0.0629	0.2487	-0.4192	-0.241	0.0319	0.26	0.0246	-0.0292	0.1583	-0.0389	0.1402	17.4791	18.9629	-28.5003
16	9.7442	-8.4869	2.5592	8.6501	-2.2626	2.3944	-0.0631	0.1878	0.225	0.2878	-0.1388	-0.1601	0.304	0.1242	0.1577	0.2607	-0.0177	-0.0316	0.1436	-0.0207	0.1862	20.9368	23.7827	-21.4577

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 434 through 456 )
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 457 through 473 )
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 474 through 493 )
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 494 through 531 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 532 through 552 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 421 through 433 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 434 through 493 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 494 through 551 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 422 through 433 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 434 through 445 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 446 through 456 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 457 through 473 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 474 through 531 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 532 through 541 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 542 through 552 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 423 through 433 )

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