[English] 日本語
Yorodumi
- PDB-2xv5: Human lamin A coil 2B fragment -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xv5
TitleHuman lamin A coil 2B fragment
ComponentsLAMIN-A/C
KeywordsSTRUCTURAL PROTEIN / INTERMEDIATE FILAMENTS / NUCLEAR MEMBRANE / LEFT-HANDED COILED COIL / RIGHT-HANDED COILED COIL
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 / Depolymerization of the Nuclear Lamina / DNA double-strand break attachment to nuclear envelope / Nuclear Envelope Breakdown / nuclear envelope organization / nuclear pore localization ...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 / Depolymerization of the Nuclear Lamina / DNA double-strand break attachment to nuclear envelope / Nuclear Envelope Breakdown / nuclear envelope organization / nuclear pore localization / lamin filament / protein localization to nuclear envelope / nuclear lamina / XBP1(S) activates chaperone genes / Initiation of Nuclear Envelope (NE) Reformation / regulation of protein localization to nucleus / nuclear migration / regulation of telomere maintenance / negative regulation of cardiac muscle hypertrophy in response to stress / muscle organ development / intermediate filament / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / negative regulation of release of cytochrome c from mitochondria / protein localization to nucleus / heterochromatin formation / regulation of cell migration / Meiotic synapsis / negative regulation of extrinsic apoptotic signaling pathway / regulation of protein stability / protein localization / structural constituent of cytoskeleton / nuclear matrix / protein import into nucleus / cellular senescence / Signaling by BRAF and RAF1 fusions / nuclear envelope / site of double-strand break / cellular response to hypoxia / nuclear membrane / nuclear speck / negative regulation of cell population proliferation / positive regulation of gene expression / structural molecule activity / perinuclear region of cytoplasm / nucleoplasm / identical protein binding / nucleus / cytosol
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 / SAD / Resolution: 2.4 Å
AuthorsKapinos, L.E. / Burkhard, P. / Aebi, U. / Herrmann, H. / Strelkov, S.V.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Simultaneous Formation of Right- and Left-Handed Anti-Parallel Coiled-Coil Interfaces by a Coil2 Fragment of Human Lamin A.
Authors: Kapinos, L.E. / Burkhard, P. / Herrmann, H. / Aebi, U. / Strelkov, S.V.
History
DepositionOct 22, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LAMIN-A/C
B: LAMIN-A/C


Theoretical massNumber of molelcules
Total (without water)17,8992
Polymers17,8992
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-19.5 kcal/mol
Surface area10080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.093, 50.114, 89.745
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.6715, 0.6537, 0.3488), (0.7062, -0.7071, -0.0343), (0.2243, 0.2694, -0.9366)
Vector: -38.8178, 52.1228, 84.6125)

-
Components

#1: Protein LAMIN-A/C / 70 KDA LAMIN / RENAL CARCINOMA ANTIGEN NY-REN-32


Mass: 8949.478 Da / Num. of mol.: 2 / Fragment: HUMAN LAMIN A FRAGMENT, RESIDUES 328-398
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02545
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.1 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growTemperature: 293 K / pH: 8.5
Details: 73% MPD, 10 MM TRIS-HCL, PH 8.5 AND 100 MM NACL, 293 K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9788
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2007 / Details: MIRRORS
RadiationMonochromator: CU FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.4→33 Å / Num. obs: 5783 / % possible obs: 97.1 % / Observed criterion σ(I): 2.4 / Redundancy: 9.9 % / Biso Wilson estimate: 49.107 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.9
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.9 / % possible all: 81.2

-
Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALEPACKdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.4→33 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.934 / SU B: 20.845 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.431 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28412 627 9.8 %RANDOM
Rwork0.24093 ---
obs0.24523 5783 97.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.087 Å2
Baniso -1Baniso -2Baniso -3
1-4.83 Å20 Å20 Å2
2--0.9 Å20 Å2
3----5.73 Å2
Refinement stepCycle: LAST / Resolution: 2.4→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms950 0 0 7 957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021969
X-RAY DIFFRACTIONr_bond_other_d0.0010.02725
X-RAY DIFFRACTIONr_angle_refined_deg1.1492.0031286
X-RAY DIFFRACTIONr_angle_other_deg0.7831744
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4295116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.07523.21456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.33115218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8551516
X-RAY DIFFRACTIONr_chiral_restr0.0560.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021065
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02199
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8591.5573
X-RAY DIFFRACTIONr_mcbond_other1.4051.5233
X-RAY DIFFRACTIONr_mcangle_it6.3922905
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it11.3673396
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it17.4794.5380
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 39 -
Rwork0.344 310 -
obs--73.01 %
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)
11.05810.8427-2.25960.8409-2.48978.9397-0.116-0.0703-0.0527-0.1415-0.0502-0.1590.3722-0.10260.16620.3290.04310.07570.16220.03080.2284-2.157631.983950.7173
23.06960.04324.84531.8165-1.962228.5415-0.2259-0.18240.03350.1643-0.1327-0.29881.09740.34040.35860.30030.0981-0.01260.0755-0.00240.22960.067124.474544.5713
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A326 - 382
2X-RAY DIFFRACTION2B326 - 382

+
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