[English] 日本語
Yorodumi
- PDB-9ul6: Crystal structure of Lamin A/C Ig-like domain mutant - R435C -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ul6
TitleCrystal structure of Lamin A/C Ig-like domain mutant - R435C
ComponentsLamin-A/C
KeywordsNUCLEAR PROTEIN / Lamin A/C / nuclear integrity / aging / laminopathies
Function / homology
Function and homology information


structural constituent of nuclear lamina / negative regulation of mesenchymal cell proliferation / protein localization to nuclear envelope / establishment or maintenance of microtubule cytoskeleton polarity / Breakdown of the nuclear lamina / ventricular cardiac muscle cell development / Depolymerization of the Nuclear Lamina / Nuclear Envelope Breakdown / nuclear pore localization / DNA double-strand break attachment to nuclear envelope ...structural constituent of nuclear lamina / negative regulation of mesenchymal cell proliferation / protein localization to nuclear envelope / establishment or maintenance of microtubule cytoskeleton polarity / Breakdown of the nuclear lamina / ventricular cardiac muscle cell development / Depolymerization of the Nuclear Lamina / Nuclear Envelope Breakdown / nuclear pore localization / DNA double-strand break attachment to nuclear envelope / lamin filament / nuclear envelope organization / XBP1(S) activates chaperone genes / nuclear lamina / Initiation of Nuclear Envelope (NE) Reformation / regulation of protein localization to nucleus / regulation of telomere maintenance / intermediate filament / negative regulation of cardiac muscle hypertrophy in response to stress / muscle organ development / nuclear migration / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / negative regulation of release of cytochrome c from mitochondria / protein localization to nucleus / regulation of cell migration / Meiotic synapsis / negative regulation of extrinsic apoptotic signaling pathway / regulation of protein stability / structural constituent of cytoskeleton / double-strand break repair via nonhomologous end joining / nuclear matrix / protein import into nucleus / cellular senescence / Signaling by BRAF and RAF1 fusions / intracellular protein localization / nuclear envelope / heterochromatin formation / site of double-strand break / nuclear membrane / cellular response to hypoxia / nuclear speck / negative regulation of cell population proliferation / positive regulation of gene expression / perinuclear region of cytoplasm / structural molecule activity / 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLee, J. / Ha, N.C.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Lamin A/C Ig-like domain mutant - R435C
Authors: Lee, J. / Ha, N.C.
History
DepositionApr 19, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,4023
Polymers48,4023
Non-polymers00
Water00
1
C: Lamin-A/C
B: Lamin-A/C


Theoretical massNumber of molelcules
Total (without water)32,2682
Polymers32,2682
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-2 kcal/mol
Surface area14100 Å2
MethodPISA
2
A: Lamin-A/C

A: Lamin-A/C


Theoretical massNumber of molelcules
Total (without water)32,2682
Polymers32,2682
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/31
Buried area1350 Å2
ΔGint-4 kcal/mol
Surface area14120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.007, 92.007, 204.805
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3

-
Components

#1: Protein Lamin-A/C / 70 kDa lamin / Renal carcinoma antigen NY-REN-32


Mass: 16133.984 Da / Num. of mol.: 3 / Mutation: R435C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LMNA, LMN1 / Production host: Escherichia coli (E. coli) / References: UniProt: P02545
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.42 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.0, 30% v/v Jeffamine ED-2001 pH 7.0

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 17639 / % possible obs: 94.8 % / Redundancy: 17.6 % / Biso Wilson estimate: 35.86 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.019 / Rrim(I) all: 0.093 / Net I/σ(I): 34.1
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 855 / CC1/2: 0.981 / Rpim(I) all: 0.07 / Rrim(I) all: 0.359

-
Processing

Software
NameVersionClassification
PHENIX1.21rc1_4933refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CRG

7crg


Resolution: 2.5→34.41 Å / SU ML: 0.3496 / Cross valid method: FREE R-VALUE / σ(F): 0.76 / Phase error: 25.9699
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2755 1722 10.06 %
Rwork0.2031 15403 -
obs0.2103 17125 92.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.39 Å2
Refinement stepCycle: LAST / Resolution: 2.5→34.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3039 0 0 0 3039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083096
X-RAY DIFFRACTIONf_angle_d0.94574197
X-RAY DIFFRACTIONf_chiral_restr0.0554468
X-RAY DIFFRACTIONf_plane_restr0.0107549
X-RAY DIFFRACTIONf_dihedral_angle_d6.8228420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.570.38511390.2911211X-RAY DIFFRACTION90.24
2.57-2.660.32551380.24291221X-RAY DIFFRACTION90.78
2.66-2.750.32831360.2371224X-RAY DIFFRACTION90.73
2.75-2.860.31791380.25041247X-RAY DIFFRACTION91.54
2.86-2.990.33791380.26481234X-RAY DIFFRACTION90.38
2.99-3.150.36051360.26271231X-RAY DIFFRACTION90.05
3.15-3.350.32381400.22681249X-RAY DIFFRACTION91.14
3.35-3.60.28361400.21081254X-RAY DIFFRACTION90.58
3.6-3.960.28531410.19581258X-RAY DIFFRACTION90.96
3.97-4.540.21861460.15371327X-RAY DIFFRACTION94
4.54-5.710.19411600.15641419X-RAY DIFFRACTION98.63
5.71-34.410.24311700.17821528X-RAY DIFFRACTION98.43

+
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://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