3gef

Crystal structure of the R482W mutant of lamin A/C

Method: X-RAY DIFFRACTION D_max: 79.7 Å Quality: EXCELLENT

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Lamin-A/C

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 436–552	Fragment：Lamin A/C globular domain Mutation：R482W Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.3；298 K；0.9M sodium citrate, 20mM DTT, 0.1M sodium cacodylate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.50 Å R-free 0.253
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 436–552	Fragment：Lamin A/C globular domain Mutation：R482W Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.3；298 K；0.9M sodium citrate, 20mM DTT, 0.1M sodium cacodylate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.50 Å R-free 0.253
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 436–552	Fragment：Lamin A/C globular domain Mutation：R482W Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.3；298 K；0.9M sodium citrate, 20mM DTT, 0.1M sodium cacodylate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.50 Å R-free 0.253
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 436–552	Fragment：Lamin A/C globular domain Mutation：R482W Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.3；298 K；0.9M sodium citrate, 20mM DTT, 0.1M sodium cacodylate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.50 Å R-free 0.253

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3GEF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1IFR Structure of Lamin A/C Globular Domain Deposited 2001-04-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 436–552（117 aa） Fragment：residues 436-552	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG4000, ammonium acetate, DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.40 Å
1IVT NMR structures of the C-terminal globular domain of human lamin A/C Deposited 2002-03-29	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 428–549（122 aa） Fragment：C-terminal domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.3；303 K；Pressure ambient NMR sample composition 1mM U-15N,13C; 20mM phosphate buffer K \| 90% H2O/10% D2O NMR sample composition 1mM U-15N; 20mM phosphate buffer K \| 90% H2O/10% D2O NMR sample composition 1mM U-15N,13C; 20mM phosphate buffer K \| 100% D2O	Resolution not provided
1X8Y Human lamin coil 2B Deposited 2004-08-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 305–387（83 aa） Fragment：human lamin A fragment (residues 305-387)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.7M Na/K tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.305
2XV5 Human lamin A coil 2B fragment Deposited 2010-10-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 328–398（71 aa） Fragment：HUMAN LAMIN A FRAGMENT, RESIDUES 328-398 Chain B 328–398（71 aa） Fragment：HUMAN LAMIN A FRAGMENT, RESIDUES 328-398	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；293 K；73% MPD, 10 MM TRIS-HCL, PH 8.5 AND 100 MM NACL, 293 K	Resolution 2.40 Å R-free 0.284
2YPT Crystal structure of the human nuclear membrane zinc metalloprotease ZMPSTE24 mutant (E336A) in complex with a synthetic CSIM tetrapeptide from the C-terminus of prelamin A Deposited 2012-11-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 661–664（4 aa） Fragment：C-TERMINAL TETRAPEPTIDE, RESIDUES 661-664	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；0.1M HEPES PH 7.0, 0.1M CALCIUM CHLORIDE, 29%(V/V) PEG 400	Resolution 3.80 Å R-free 0.281
2YPT Crystal structure of the human nuclear membrane zinc metalloprotease ZMPSTE24 mutant (E336A) in complex with a synthetic CSIM tetrapeptide from the C-terminus of prelamin A Deposited 2012-11-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 661–664（4 aa） Fragment：C-TERMINAL TETRAPEPTIDE, RESIDUES 661-664	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；0.1M HEPES PH 7.0, 0.1M CALCIUM CHLORIDE, 29%(V/V) PEG 400	Resolution 3.80 Å R-free 0.281
2YPT Crystal structure of the human nuclear membrane zinc metalloprotease ZMPSTE24 mutant (E336A) in complex with a synthetic CSIM tetrapeptide from the C-terminus of prelamin A Deposited 2012-11-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 661–664（4 aa） Fragment：C-TERMINAL TETRAPEPTIDE, RESIDUES 661-664	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；0.1M HEPES PH 7.0, 0.1M CALCIUM CHLORIDE, 29%(V/V) PEG 400	Resolution 3.80 Å R-free 0.281
2YPT Crystal structure of the human nuclear membrane zinc metalloprotease ZMPSTE24 mutant (E336A) in complex with a synthetic CSIM tetrapeptide from the C-terminus of prelamin A Deposited 2012-11-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 661–664（4 aa） Fragment：C-TERMINAL TETRAPEPTIDE, RESIDUES 661-664	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；0.1M HEPES PH 7.0, 0.1M CALCIUM CHLORIDE, 29%(V/V) PEG 400	Resolution 3.80 Å R-free 0.281
3V4Q Structure of R335W mutant of human Lamin Deposited 2011-12-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 313–386（74 aa） Fragment：Coil 2b	Mutation：R335W	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；15% Ethanol, 0.1M Citrate pH 5.5, 0.2 M Litium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 3.06 Å R-free 0.282
3V4Q Structure of R335W mutant of human Lamin Deposited 2011-12-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 313–386（74 aa） Fragment：Coil 2b	Mutation：R335W	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；15% Ethanol, 0.1M Citrate pH 5.5, 0.2 M Litium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 3.06 Å R-free 0.282
3V4W Structure of E347K mutant of Lamin Deposited 2011-12-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 313–386（74 aa） Fragment：Coil 2b	Mutation：E347K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；30% 2-methyl-2,4-pentanediol, 0.1 M Sodium Acetate pH 4.6, 0.2 M Sodium Chloride, VAPOR DIFFUSION, SITTING DROP	Resolution 3.70 Å R-free 0.339
3V4W Structure of E347K mutant of Lamin Deposited 2011-12-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 313–386（74 aa） Fragment：Coil 2b	Mutation：E347K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；30% 2-methyl-2,4-pentanediol, 0.1 M Sodium Acetate pH 4.6, 0.2 M Sodium Chloride, VAPOR DIFFUSION, SITTING DROP	Resolution 3.70 Å R-free 0.339
3V5B Structure of Coil 2b of human lamin Deposited 2011-12-16	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 313–386（74 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；30% 2-methyl-2,4-pentanediol, 0.1 M Hepes pH 7.5, 0.5 M Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP	Resolution 3.00 Å R-free 0.326
3V5B Structure of Coil 2b of human lamin Deposited 2011-12-16	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 313–386（74 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；30% 2-methyl-2,4-pentanediol, 0.1 M Hepes pH 7.5, 0.5 M Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP	Resolution 3.00 Å R-free 0.326
6GHD Structural analysis of the ternary complex between lamin A/C, BAF and emerin identifies an interface disrupted in autosomal recessive progeroid diseases Deposited 2018-05-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 428–546（119 aa）	Not recorded	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；25% PEG3.350, 20mM Tris-BispH5.5, 30mM NaCl, 0.2M NH4SO4	Resolution 2.10 Å R-free 0.247
6GHD Structural analysis of the ternary complex between lamin A/C, BAF and emerin identifies an interface disrupted in autosomal recessive progeroid diseases Deposited 2018-05-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain F 428–546（119 aa）	Not recorded	SO4 SULFATE ION × 3 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；25% PEG3.350, 20mM Tris-BispH5.5, 30mM NaCl, 0.2M NH4SO4	Resolution 2.10 Å R-free 0.247
6JLB Crystal structure of lamin A/C fragment and assembly mechanisms of intermediate filaments Deposited 2019-03-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–300（300 aa） Chain B 1–300（300 aa） Chain C 1–300（300 aa） Chain D 1–300（300 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；287 K；0.1 M Tris-HCl (pH 8.5), 0.9 M Lithium chloride, 7% (v/v) PEG 8000	Resolution 3.21 Å R-free 0.261
6RPR LEM domain of Emerin mutant T43I in complex with BAF dimer and the Igfold of the lamin A/C Deposited 2019-05-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 318–433（116 aa）	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；18% PEG 3350, 100 mM Tris Bis pH 5.5, 0.1 M NH4SO4	Resolution 2.26 Å R-free 0.244
6SNZ Crystal structure of lamin A coil1b tetramer Deposited 2019-08-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 65–222（158 aa） Chain B 65–222（158 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 8K 10%, Imodazole 0.1M, Calcium acetate 0.2M	Resolution 2.60 Å R-free 0.281
6SNZ Crystal structure of lamin A coil1b tetramer Deposited 2019-08-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 65–222（158 aa） Chain D 65–222（158 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 8K 10%, Imodazole 0.1M, Calcium acetate 0.2M	Resolution 2.60 Å R-free 0.281
6YF5 Lamin A 17-70 coil1A dimer stabilized by C-terminal capping Deposited 2020-03-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 17–70（54 aa） Chain B 17–70（54 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.9；277 K；35.7% (w/v) 1,6-hexanediol, 5% (w/v) PEG 1K and 0.1 M trisodium citrate dihydrate	Resolution 1.83 Å R-free 0.255
6YF5 Lamin A 17-70 coil1A dimer stabilized by C-terminal capping Deposited 2020-03-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 17–70（54 aa） Chain D 17–70（54 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.9；277 K；35.7% (w/v) 1,6-hexanediol, 5% (w/v) PEG 1K and 0.1 M trisodium citrate dihydrate	Resolution 1.83 Å R-free 0.255
6YJD Lamin A coil2 dimer stabilized by N-terminal capping Deposited 2020-04-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 326–403（78 aa）	Mutation：F40C	NI NICKEL (II) ION × 4 CL CHLORIDE ION × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；277 K；35% (v/v) methanol, 0.2 M MgCl2 and 0.1 M HEPES	Resolution 2.90 Å R-free 0.304
6YSH Lamin A 1-70 coil1A dimer stabilized by C-terminal capping Deposited 2020-04-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 25–70（46 aa） Chain B 26–70（45 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；0.1M NaH2PO4 H2O,0.1M KH2PO4,2.0M NaCl,0.1M Mes H20 pH 6	Resolution 2.83 Å R-free 0.281
7CRG Beta-strand-mediated dimeric formation of the extended Ig-like domains of human lamin A/C Deposited 2020-08-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 406–553（148 aa） Chain C 406–553（148 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；287 K；0.2 M Potassium Chloride, 0.05 M HEPES pH 7.5, 35%(v/v) Pentaerythritol Propoxylate (5/4PO/OH)	Resolution 1.80 Å R-free 0.216
7CRG Beta-strand-mediated dimeric formation of the extended Ig-like domains of human lamin A/C Deposited 2020-08-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 406–553（148 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；287 K；0.2 M Potassium Chloride, 0.05 M HEPES pH 7.5, 35%(v/v) Pentaerythritol Propoxylate (5/4PO/OH)	Resolution 1.80 Å R-free 0.216
7D9N Crystal structure of a non-canonic progeria mutation S143F at lamin A/C and its structural implication to the premature aging Deposited 2020-10-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 27–229（203 aa） Chain B 27–229（203 aa）	Mutation：S143F Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：S143F Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；287 K；0.2 M Tris-Hcl pH8 0.1 M Sodium citrate 18% PEG 400	Resolution 3.70 Å R-free 0.304
7X5D Crystal Structure of the K316C mutant of Human Lamin A/C Coil 2 (residues 244-340) Deposited 2022-03-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 244–339（96 aa） Chain B 244–339（96 aa）	Mutation：K316C Mutation：K316C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；287 K；Tacsimate (pH 5.5), PEG 3350, methyl mercury acetate	Resolution 1.82 Å R-free 0.279
7YVD The crystal structure of the progerin C-terminal peptide and the Ig-like domain of lamin A/C Deposited 2022-08-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 421–552（132 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SEC SELENOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；287 K；0.1 M BIS-TRIS pH 6.5, 25% (v/v) Polyethylene glycol 300	Resolution 2.10 Å R-free 0.195
7YVD The crystal structure of the progerin C-terminal peptide and the Ig-like domain of lamin A/C Deposited 2022-08-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 421–552（132 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SEC SELENOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；287 K；0.1 M BIS-TRIS pH 6.5, 25% (v/v) Polyethylene glycol 300	Resolution 2.10 Å R-free 0.195
7YVD The crystal structure of the progerin C-terminal peptide and the Ig-like domain of lamin A/C Deposited 2022-08-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 421–552（132 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SEC SELENOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；287 K；0.1 M BIS-TRIS pH 6.5, 25% (v/v) Polyethylene glycol 300	Resolution 2.10 Å R-free 0.195
7Z21 BAF A12T bound to the lamin A/C Ig-fold domain Deposited 2022-02-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 411–566（156 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；3 M ammonium sulfate 0.1 M bicine pH 9	Resolution 1.63 Å R-free 0.300
7Z21 BAF A12T bound to the lamin A/C Ig-fold domain Deposited 2022-02-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 411–566（156 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；3 M ammonium sulfate 0.1 M bicine pH 9	Resolution 1.63 Å R-free 0.300
9J8M Cryo-EM structure of BAF-Lamin A/C IgF-nucleosome complex (High mobility complex) Deposited 2024-08-21	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric	Chain M 411–566（156 aa） Fragment：Ig-fold domain	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.82 Å
9J8N Cryo-EM structure of BAF-Lamin A/C IgF-nucleosome complex (Low mobility complex) Deposited 2024-08-21	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 32-meric	Chain M 411–566（156 aa） Fragment：Ig-fold domain Chain P 411–566（156 aa） Fragment：Ig-fold domain Chain m 411–566（156 aa） Fragment：Ig-fold domain Chain p 411–566（156 aa） Fragment：Ig-fold domain	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.14 Å
9J8O Cryo-EM structure of BAF-Lamin A/C IgF-H1-nucleosome complex Deposited 2024-08-21	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 28-meric	Chain M 411–566（156 aa） Fragment：Ig-fold domain Chain m 411–566（156 aa） Fragment：Ig-fold domain	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.05 Å
9UL6 Crystal structure of Lamin A/C Ig-like domain mutant - R435C Deposited 2025-04-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 406–552（147 aa） Chain C 406–552（147 aa）	Mutation：R435C Mutation：R435C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；287 K；0.1 M Sodium citrate tribasic dihydrate pH 5.0, 30% v/v Jeffamine ED-2001 pH 7.0	Resolution 2.50 Å R-free 0.276
9UL6 Crystal structure of Lamin A/C Ig-like domain mutant - R435C Deposited 2025-04-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 406–552（147 aa）	Mutation：R435C	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；287 K；0.1 M Sodium citrate tribasic dihydrate pH 5.0, 30% v/v Jeffamine ED-2001 pH 7.0	Resolution 2.50 Å R-free 0.276

24 other PDB entries and 38 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LMNA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–118； UniProt 436–552 Author chain B； PDBConstruct 2–118； UniProt 436–552 Author chain C； PDBConstruct 2–118； UniProt 436–552 Author chain D； PDBConstruct 2–118； UniProt 436–552

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3gef
Deposition date deposition_date	2009-02-25
Structure title title	Crystal structure of the R482W mutant of lamin A/C
Keywords keywords	;immunoglobulin fold, lamin, Cardiomyopathy, Charcot-Marie-Tooth disease, Disease mutation, Intermediate filament, Limb-girdle muscular dystrophy, Lipoprotein, Nucleus, Phosphoprotein, Prenylation, STRUCTURAL PROTEIN ;; STRUCTURAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	25.95 Å
Radius of gyration Rg (electron density) rg_electron	25.27 Å
Forward intensity I(0) i0	48707700.00
Molecular weight molecular_weight	52149.0 kDa
Excluded volume excluded_volume	64602 Å³
Envelope volume envelope_volume	81442 Å³
Hydration-shell volume shell_volume	27291 Å³
Envelope diameter envelope_diameter	84.5 Å
Shell Rg shell_rg	31.96 Å
Envelope Rg envelope_rg	24.92 Å
Shape Rg shape_rg	25.30 Å
Total Rg total_rg	25.94 Å
Total atoms total_atoms	3672
Residues n_residues	468
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	79.7 Å
Rg (real space) rg_real	25.86 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	4.8710e+07
I(0) uncertainty (real space) i0_real_error	6.8550e+05
Rg (reciprocal space) rg_reciprocal	25.89 Å
I(0) (reciprocal space) i0_reciprocal	48710000.0000
Solution quality estimate total_estimate	0.9140
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.8 Å
Skewness Skewness skewness	0.183
Kurtosis Kurtosis kurtosis	-0.599
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10070000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.963; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.988

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3gefa1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.16 — Lamin A/C globular tail domain
Family Family family	b.1.16.1 — Lamin A/C globular tail domain

Domain ID domain_id	d3gefa2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3gefb1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.16 — Lamin A/C globular tail domain
Family Family family	b.1.16.1 — Lamin A/C globular tail domain

Domain ID domain_id	d3gefb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3gefc1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.16 — Lamin A/C globular tail domain
Family Family family	b.1.16.1 — Lamin A/C globular tail domain

Domain ID domain_id	d3gefc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3gefd1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.16 — Lamin A/C globular tail domain
Family Family family	b.1.16.1 — Lamin A/C globular tail domain

Domain ID domain_id	d3gefd2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	3gefA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1260 — Lamin Tail domain

Domain ID domain_id	3gefB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1260 — Lamin Tail domain

Domain ID domain_id	3gefC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1260 — Lamin Tail domain

Domain ID domain_id	3gefD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1260 — Lamin Tail domain

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8. Citations (1)

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Unit-cell length a length_a	62.195 Å
Unit-cell length b length_b	84.035 Å
Unit-cell length c length_c	98.750 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	45.000 Å
R factor r_factor	—
R_work r_work	0.2141
R_free r_free	0.2531

Description description	Lamin-A/C
Molecular weight formula_weight	13094.6 kDa
Mutation mutation	R482W
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	3992

Crystal structure of the R482W mutant of lamin A/C

1. Protein Identity and Related Structures Protein Identity & Related Structures

Lamin-A/C

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	320

fit	/app/data/saxs_computation/ge/3gef/3gef.fit
pddf	/app/data/pr_computation/ge/3gef/3gef.pr.out
profile	/app/data/saxs_computation/ge/3gef/3gef.dat