[English] 日本語
Yorodumi
- PDB-3tyy: Crystal Structure of Human Lamin-B1 Coil 2 Segment -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tyy
TitleCrystal Structure of Human Lamin-B1 Coil 2 Segment
ComponentsLamin-B1
KeywordsSTRUCTURAL PROTEIN / Lamin-B1 / LMNB1 / B-type lamins / intermediate filament (IF) / membrane / nucleus / Structural Genomics Consortium / SGC
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 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 ...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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.399 Å
AuthorsLam, R. / Xu, C. / Bian, C.B. / Mackenzie, F. / Walker, J.R. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. ...Lam, R. / Xu, C. / Bian, C.B. / Mackenzie, F. / Walker, J.R. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: 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
DepositionSep 26, 2011Deposition site: RCSB / Processing site: RCSB
SupersessionOct 5, 2011ID: 3MOV
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lamin-B1
B: Lamin-B1


Theoretical massNumber of molelcules
Total (without water)23,1422
Polymers23,1422
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-39 kcal/mol
Surface area11030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.982, 45.982, 203.231
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Lamin-B1


Mass: 11570.989 Da / Num. of mol.: 2 / Fragment: Coil 2 (UNP RESIDUES: 311-388)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LMN2, LMNB, LMNB1 / Plasmid: PET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P20700
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG3350, 0.2M LISO4, 0.1M BIS-TRIS pH 6.5, 0.1M CrCl3, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97944 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 13, 2010 / Details: Si(111) Double Crystal Monochrometer
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97944 Å / Relative weight: 1
ReflectionResolution: 2.399→50 Å / Num. obs: 10417 / % possible obs: 98.9 % / Redundancy: 11.7 % / Rmerge(I) obs: 0.068 / Χ2: 0.997 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.399-2.4911.40.5079890.904198.4
2.49-2.5912.20.37910020.952198.6
2.59-2.712.10.30510390.991199.1
2.7-2.85120.24110161.028198.8
2.85-3.0212.20.14710001.025198.8
3.02-3.26120.10510251198.8
3.26-3.5811.80.07210400.994199.4
3.58-4.111.70.04510550.998199.3
4.1-5.1711.50.03510831.038199.1
5.17-5010.40.0311681.034198.6

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 59.78 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å37.08 Å
Translation2.5 Å37.08 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefmac_5.6.0117refinement
PDB_EXTRACT3.1data extraction
Locallymodified Blu-Ice GUI interface to EPICS controldata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X8Y

1x8y


Resolution: 2.399→37.08 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.253 / WRfactor Rwork: 0.235 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 14.406 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.288 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2611 484 4.7 %RANDOM
Rwork0.2353 ---
obs0.2365 10400 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 117.73 Å2 / Biso mean: 59.9235 Å2 / Biso min: 35.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.399→37.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1212 0 0 18 1230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191230
X-RAY DIFFRACTIONr_angle_refined_deg1.4732.0091639
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1745148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.3325.40574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.88215280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0681515
X-RAY DIFFRACTIONr_chiral_restr0.10.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02911
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.399-2.4610.385330.31858162797.927
2.461-2.5280.339310.30659663798.43
2.528-2.6010.342450.30155961198.854
2.601-2.6810.365240.27256058999.151
2.681-2.7680.273210.26754657299.126
2.768-2.8650.225240.29852755898.746
2.865-2.9720.379170.29749952199.04
2.972-3.0930.339320.28746950898.622
3.093-3.2290.288130.25946448199.168
3.229-3.3860.282320.243423455100
3.386-3.5670.265130.23743344999.332
3.567-3.7810.3170.21638940799.754
3.781-4.0390.232160.19534936699.727
4.039-4.3590.204170.18633935799.72
4.359-4.7680.193190.17429231299.679
4.768-5.320.226150.19526928699.301
5.32-6.1220.30390.28523824899.597
6.122-7.4470.42350.239195200100
7.447-10.3260.21150.191135140100
10.326-37.0760.11230.199667295.833
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.01680.0477-0.03740.5002-2.079911.10440.0119-0.0015-0.00820.0415-0.0049-0.0116-0.16460.029-0.0070.0430.0152-0.02680.11750.03460.100511.11-17.6361.004
20.1143-0.28761.23140.82-3.067713.5289-0.03280.02920.01750.098-0.1339-0.0536-0.43480.34770.16670.0645-0.0447-0.04690.06560.01420.114215.862-12.4531.966
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A311 - 385
2X-RAY DIFFRACTION2B313 - 383

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more