[English] 日本語
Yorodumi
- PDB-2q1n: Actin Dimer Cross-linked Between Residues 41 and 374 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2q1n
TitleActin Dimer Cross-linked Between Residues 41 and 374
ComponentsActin, alpha skeletal muscle
KeywordsSTRUCTURAL PROTEIN / cross-linked dimer
Function / homology
Function and homology information


cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament ...cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family ...ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / LATRUNCULIN A / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSawaya, M.R. / Pashkov, I. / Kudryashov, D.S. / Adisetiyo, H. / Reisler, E. / Yeates, T.O.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Multiple crystal structures of actin dimers and their implications for interactions in the actin filament.
Authors: Sawaya, M.R. / Kudryashov, D.S. / Pashkov, I. / Adisetiyo, H. / Reisler, E. / Yeates, T.O.
History
DepositionMay 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Actin, alpha skeletal muscle
B: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,74110
Polymers83,7252
Non-polymers2,0168
Water41423
1
A: Actin, alpha skeletal muscle
hetero molecules

A: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,74110
Polymers83,7252
Non-polymers2,0168
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
2
B: Actin, alpha skeletal muscle
hetero molecules

B: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,74110
Polymers83,7252
Non-polymers2,0168
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Unit cell
Length a, b, c (Å)108.057, 71.813, 54.787
Angle α, β, γ (deg.)90.000, 104.700, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LAR / End label comp-ID: LAR / Refine code: 2 / Auth seq-ID: 4 - 403 / Label seq-ID: 4

Dom-IDAuth asym-IDLabel asym-ID
1AA - F
2BB - J
DetailsA unit cell translation along the "c" axis generates the cross-linked dimer.

-
Components

#1: Protein Actin, alpha skeletal muscle / / Alpha-actin-1


Mass: 41862.613 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-LAR / LATRUNCULIN A / 4-(17-HYDROXY-5,12-DIMETHYL-3-OXO-2,16-DIOXABICYCLO[13.3.1]NONADECA-4,8,10-TRIEN-17-YL)-2-THIAZOLIDINONE / Latrunculin


Mass: 421.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H31NO5S / Comment: toxin*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.45 Å3/Da / Density % sol: 49.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 30% MPD, 0.1M sodium acetate, 0.02 M calcium chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2005
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→90 Å / Num. all: 23524 / Num. obs: 23524 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 71.8 Å2 / Rmerge(I) obs: 0.093 / Χ2: 1.038 / Net I/σ(I): 9.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3 % / Rmerge(I) obs: 0.471 / Num. unique all: 2291 / Χ2: 1.035 / % possible all: 97.1

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
BOSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2A5X

2a5x


Resolution: 2.7→52.26 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.876 / SU B: 30.078 / SU ML: 0.34 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1147 5.1 %RANDOM
Rwork0.228 ---
all0.231 22428 --
obs0.231 22428 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.45 Å2
Baniso -1Baniso -2Baniso -3
1--7.56 Å20 Å2-1.07 Å2
2--6.18 Å20 Å2
3---0.84 Å2
Refinement stepCycle: LAST / Resolution: 2.7→52.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5401 0 124 23 5548
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225649
X-RAY DIFFRACTIONr_bond_other_d0.0020.023789
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.9897682
X-RAY DIFFRACTIONr_angle_other_deg0.87639260
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.755685
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.18623.975239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62315945
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1171533
X-RAY DIFFRACTIONr_chiral_restr0.0680.2861
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026162
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021107
X-RAY DIFFRACTIONr_nbd_refined0.20.21274
X-RAY DIFFRACTIONr_nbd_other0.1850.23978
X-RAY DIFFRACTIONr_nbtor_refined0.1750.22764
X-RAY DIFFRACTIONr_nbtor_other0.0810.22842
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2149
X-RAY DIFFRACTIONr_metal_ion_refined0.1830.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2130.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.26
X-RAY DIFFRACTIONr_mcbond_it2.16823579
X-RAY DIFFRACTIONr_mcbond_other0.43721384
X-RAY DIFFRACTIONr_mcangle_it3.06535568
X-RAY DIFFRACTIONr_scbond_it2.51122428
X-RAY DIFFRACTIONr_scangle_it3.532114
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
2023TIGHT POSITIONAL0.020.05
2622MEDIUM POSITIONAL0.210.5
2023TIGHT THERMAL0.110.5
2622MEDIUM THERMAL0.492
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 72 -
Rwork0.32 1563 -
obs-1635 98.49 %
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)
16.8959-0.04390.25991.33110.96763.9033-0.0955-0.2328-0.27970.1057-0.04070.35390.0657-0.49460.1362-0.1846-0.0917-0.0023-0.19140.04980.041719.663830.07816.5649
26.05911.19552.8151.9077-0.34264.8774-0.11340.8257-0.1576-0.35160.190.02640.06120.3929-0.0766-0.2039-0.10280.0176-0.12620.0472-0.214243.31233.27398.3532
313.52250.0563-0.81713.0884-0.0360.0497-0.0313-1.60980.56580.1818-0.0462-0.0667-0.0491-0.46980.0775-0.0808-0.03330.0256-0.1416-0.0312-0.247645.9939.749531.9341
44.96-1.1537-0.16741.27370.73724.5503-0.08020.54950.274-0.2436-0.0730.3718-0.2045-0.15040.1532-0.1540.0442-0.1059-0.19450.09330.0811-4.54694.254115.6947
57.4007-1.00090.41931.6405-0.29462.8708-0.2495-0.970.0290.30640.28220.3399-0.1788-0.1236-0.0326-0.18270.10210.04530.02420.1045-0.231812.07621.122934.4453
67.6339-0.66452.89950.9565-0.27953.15120.14771.1695-0.427-0.15250.0402-0.11480.2721-0.2266-0.1879-0.14060.01640.0463-0.0276-0.068-0.23725.9723-5.362115.2067
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 375 - 37
2X-RAY DIFFRACTION1AA66 - 13766 - 137
3X-RAY DIFFRACTION1AA337 - 347337 - 347
4X-RAY DIFFRACTION2AA138 - 181138 - 181
5X-RAY DIFFRACTION2AA263 - 336263 - 336
6X-RAY DIFFRACTION3AA182 - 262182 - 262
7X-RAY DIFFRACTION4BB5 - 375 - 37
8X-RAY DIFFRACTION4BB66 - 13766 - 137
9X-RAY DIFFRACTION4BB337 - 347337 - 347
10X-RAY DIFFRACTION5BB138 - 181138 - 181
11X-RAY DIFFRACTION5BB263 - 336263 - 336
12X-RAY DIFFRACTION6BB182 - 262182 - 262

+
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