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- PDB-2kpw: NMR solution structure of Lamin-B1 protein from Homo sapiens: Nor... -

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Basic information

Entry
Database: PDB / ID: 2kpw
TitleNMR solution structure of Lamin-B1 protein from Homo sapiens: Northeast Structural Genomics Consortium MEGA target, HR5546A (439-549)
ComponentsLamin-B1
KeywordsSTRUCTURAL PROTEIN / PSI-2 / NESG / HR5546A / Lamin-B1 / GFT / Acetylation / Chromosomal rearrangement / Coiled coil / Intermediate filament / Leukodystrophy / Lipoprotein / Membrane / Nucleus / Phosphoprotein / Polymorphism / Prenylation / Structural Genomics / Protein Structure Initiative / Northeast Structural Genomics Consortium
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 ...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 / RHOF GTPase cycle / RHOD GTPase cycle / nuclear migration / nuclear inner membrane / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / phospholipase binding / heterochromatin formation / Meiotic synapsis / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / structural constituent of cytoskeleton / nuclear matrix / sequence-specific double-stranded DNA binding / nuclear envelope / nuclear membrane / nucleoplasm / membrane / nucleus
Similarity search - Function
Lamin Tail domain / Lamin tail domain superfamily / Lamin tail domain / Lamin Tail Domain / Lamin-tail (LTD) domain profile. / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. ...Lamin Tail domain / Lamin tail domain superfamily / Lamin tail domain / Lamin Tail Domain / Lamin-tail (LTD) domain profile. / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. / Intermediate filament protein / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSwapna, G.V.T. / Ciccosanti, C.L. / Belote, R. / Hamilton, K. / Acton, T. / Huang, Y. / Xiao, R. / Everett, J. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR solution structure of Lamin-B1 protein from Homo sapiens: Northeast Structural Genomics Consortium target, HR5546A (439-549)
Authors: Swapna, G.V.T. / Ciccosanti, C. / Belote, R.L. / Hamilton, K. / Acton, T. / Huang, Y. / Xiao, R. / Everett, J. / Montelione, G.T.
History
DepositionOct 21, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: pdbx_database_status / pdbx_nmr_representative ...pdbx_database_status / pdbx_nmr_representative / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_representative.selection_criteria ..._pdbx_database_status.status_code_cs / _pdbx_nmr_representative.selection_criteria / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Aug 18, 2021Group: Database references / Experimental preparation / Structure summary
Category: database_2 / pdbx_nmr_exptl_sample ...database_2 / pdbx_nmr_exptl_sample / pdbx_nmr_sample_details / struct
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.pdbx_model_details
Revision 1.4Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.5May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lamin-B1


Theoretical massNumber of molelcules
Total (without water)13,6721
Polymers13,6721
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Lamin-B1


Mass: 13672.312 Da / Num. of mol.: 1 / Fragment: sequence database residues 439-549
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LMN2, LMNB, LMNB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: P20700

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
2212D 1H-13C HSQC
3313D HN(CA)CB
4413D CBCA(CO)NH
5513D HBHA(CO)NH
6613D HNCO
7713D HNHA
8813D (H)CCH-TOCSY
9913D 1H-15N NOESY
101013D 1H-13C NOESY
111112D HNOE
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE SPECTROSCOPY. DATA FOR THE BACKBONE ASSIGNMENTS WAS ACQUIRED USING GFT NMR EXPERIMENTS. AUTOMATED RESONANCE ASSIGNMENTS WERE MADE USING ...Text: THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE SPECTROSCOPY. DATA FOR THE BACKBONE ASSIGNMENTS WAS ACQUIRED USING GFT NMR EXPERIMENTS. AUTOMATED RESONANCE ASSIGNMENTS WERE MADE USING AUTOASSIGN AND PATTERN-PICKER ALGORITHMS DEVELOPED FOR AUTOMATED ASSIGNMENTS OF GFT DATA. SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATED NOESY ASSIGNMENTS WERE MADE USING AUTOSTRUCTURE AND STRUCTURE SOLUTION WAS DETERMINED USING CYANA-2.1. 100 STRUCTURES WERE CALCULATED AND 20 BEST CONFORMERS WERE THEN REFINED IN A SHELL OF WATER USING CNS. INITIAL DIHEDRAL ANGLE CONSTRIANTS WERE OBTAINED FROM TALOS. COMPLETENESS OF THE ASSIGNMENTS INCLUDING THE N-TERMINAL 6XHIS TAG WERE BACKBONE:99% SIDECHAIN: 96%. THE ASSIGNMENTS WERE VALIDATED USING AVS SOFTWARE.

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Sample preparation

DetailsType: solution
Contents: 1.129 MM [U-100% 13C; U-100% 15N] LAMIN-B1 PROTEIN, 90% H2O/10% D2O
Label: 1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.129 mM / Component: Lamin-B1 protein / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 20mM NH4OAc, 5mM CACL2, 200mM NACL / pH: 4.5 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
CNS2.0.6BRUNGER, ADAMS, CLORE, GROS, NILGES AND READrefinement
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
AVSMoseley and Montelionechemical shift assignment
NMRPipe2008Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky2.3Goddardpeak picking
AutoStructure2.2.1Huang, Tejero, Powers and Montelionestructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichgeometry optimization
TopSpin2.1Bruker Biospincollection
VnmrJ2.1Variancollection
Sparky2.3Goddarddata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 1
Details: FINAL STRUCTURE QUALITY FACTORS DETERMINED USING PSVS SOFTWARE: ORDERED RESIDUES ARE DEFINED AS:15A-32A,34A-37A,42A-47A,53A-72A,75A-79A,85A-91A,101A-106A, 110A-116A.(A) RMSD(ORDERED RESIDUES) ...Details: FINAL STRUCTURE QUALITY FACTORS DETERMINED USING PSVS SOFTWARE: ORDERED RESIDUES ARE DEFINED AS:15A-32A,34A-37A,42A-47A,53A-72A,75A-79A,85A-91A,101A-106A, 110A-116A.(A) RMSD(ORDERED RESIDUES):BACKBONE ATOMS: 0.7A; ALL ATOMS: 1.0A.(B) RAMACHANDRAN STATISTICS FOR ALL ORDERED RESIDUES: MOST FAVOURED REGIONS: 83.1% ADDITIONALLY ALLOWED REGIONS:16.9% (C) PROCHECK SCORES FOR ALL ORDERED RESIDUES (RAW/Z): PHI-PSI -0.76/-2.68, ALL: -0.42/-2.48 (D) MOLPROBITY CLASH SCORE (RAW/Z): 20.38/-1.97. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA: RECALL:0.962 PRECISION: 0.919 F-MEASURE: 0.94 DP-SCORE 0.794.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20
NMR ensemble rmsDistance rms dev: 0 Å

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