[English] 日本語
Yorodumi
- PDB-1qs7: The 1.8 angstrom structure of calmodulin rs20 peptide complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qs7
TitleThe 1.8 angstrom structure of calmodulin rs20 peptide complex
Components
  • CALMODULIN
  • RS20
KeywordsMETAL BINDING PROTEIN/PEPTIDE / CALMODULIN / CALCIUM BINDING / HELIX-LOOP-HELIX / SIGNALLING / COMPLEX(CALCIUM-BINDING PROTEIN-PEPTIDE) / METAL BINDING PROTEIN-PEPTIDE COMPLEX
Function / homology
Function and homology information


tonic smooth muscle contraction / myosin-light-chain kinase / myosin light chain kinase activity / myosin II complex / cleavage furrow / stress fiber / lamellipodium / calmodulin binding / calcium ion binding / ATP binding ...tonic smooth muscle contraction / myosin-light-chain kinase / myosin light chain kinase activity / myosin II complex / cleavage furrow / stress fiber / lamellipodium / calmodulin binding / calcium ion binding / ATP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Myosin Light Chain Kinase 1, Kinase domain / Unstructured linker between I-set domains 2 and 3 on MYLCK / Immunoglobulin I-set / Immunoglobulin I-set domain / EF-hand / : / Recoverin; domain 1 / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 ...Myosin Light Chain Kinase 1, Kinase domain / Unstructured linker between I-set domains 2 and 3 on MYLCK / Immunoglobulin I-set / Immunoglobulin I-set domain / EF-hand / : / Recoverin; domain 1 / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / EF-hand domain pair / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / EF-hand domain-containing protein / Myosin light chain kinase, smooth muscle / Myosin light chain kinase, smooth muscle
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWeigand, S. / Anderson, W.F.
Citation
Journal: To be Published
Title: High Resolution Structure of a Calmodulin Rs20 Peptide Complex
Authors: Weigand, S. / Shuvalova, L. / Lukas, T.J. / Mirzoeva, S. / Watterson, D.M. / Anderson, W.F.
#1: Journal: Biochemistry / Year: 1999
Title: Analysis of the Functional Coupling between Calmodulin's Calcium Binding and Peptide Recognition Properties
Authors: Mirzoeva, S. / Weigand, S. / Lukas, T.J. / Shuvalova, L. / Anderson, W.F. / Watterson, D.M.
#2: Journal: Science / Year: 1992
Title: Target Enzyme Recognition by Calmodulin: 2.4 A Structure of a Calmodulin- Peptide Complex
Authors: Meador, W.E. / Means, A.R. / Quiocho, F.A.
History
DepositionJun 25, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / 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_alt_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CALMODULIN
B: RS20
C: CALMODULIN
D: RS20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,63212
Polymers37,3114
Non-polymers3218
Water4,756264
1
A: CALMODULIN
B: RS20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8166
Polymers18,6562
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-72 kcal/mol
Surface area8600 Å2
MethodPISA
2
C: CALMODULIN
D: RS20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8166
Polymers18,6562
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-62 kcal/mol
Surface area8490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.016, 54.481, 66.304
Angle α, β, γ (deg.)90.00, 92.759, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein CALMODULIN


Mass: 16327.974 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Description: Synthetic Construct / Plasmid: PVUCH-1 / Production host: Escherichia coli (E. coli) / Strain (production host): UT481 / References: GenBank: 208092, UniProt: A0MMD0*PLUS
#2: Protein/peptide RS20


Mass: 2327.696 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: PEPTIDE ANALOG OF THE CALMODULIN RECOGNITION REGION OF CHICKEN SMOOTH MUSCLE/ NONMUSCLE MYOSIN LIGHT CHAIN KINASE
References: UniProt: P19038, UniProt: P11799*PLUS
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE PRESENCE OR ABSENCE OF THE FORMYL BLOCKING GROUP ON TRYPTOPHAN-4 OF THE PEPTIDE HAS NO EFFECT ...THE PRESENCE OR ABSENCE OF THE FORMYL BLOCKING GROUP ON TRYPTOPHAN-4 OF THE PEPTIDE HAS NO EFFECT ON THE CALCIUM BINDING PROPERTIES OF THE WILD-TYPE CALMODULIN. (UNPUBLISHED)
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 20% (W/V) PEG 8000, 50 MM SODIUM ACETATE 5 MM CALCIUM CHLORIDE 0.01% (W/V) SODIUM AZIDE, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 107 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 7, 1995 / Details: COLLIMATOR
RadiationMonochromator: FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.59→28.87 Å / Num. all: 39297 / Num. obs: 32557 / % possible obs: 82.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 24
Reflection shellResolution: 1.59→1.84 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 8.6 / % possible all: 91.8

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VRK

1vrk


Resolution: 1.8→28.87 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1057648.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
Stereochemistry target values: ENGH, R.A. AND HUBER, R. (1991). ACTA CRYST. A47, 392-400.
RfactorNum. reflection% reflectionSelection details
Rfree0.259 2493 9.7 %RANDOM
Rwork0.228 ---
obs0.228 25684 94.4 %-
all-27212 --
Displacement parametersBiso mean: 26 Å2
Baniso -1Baniso -2Baniso -3
1-6.86 Å20 Å20.6 Å2
2---1.66 Å20 Å2
3----5.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.8→28.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2587 0 8 264 2859
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.16
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.071.5
X-RAY DIFFRACTIONc_mcangle_it3.342
X-RAY DIFFRACTIONc_scbond_it2.072
X-RAY DIFFRACTIONc_scangle_it3.152.5
LS refinement shellResolution: 1.8→1.85 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.408 167 9.4 %
Rwork0.373 1608 -
obs--92.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1MYCNSLIB:PROTEIN.PARAMMYCNSLIB:PROTEIN.TOP
X-RAY DIFFRACTION2MYCNSLIB:ION.PARAMWATER.TOP
X-RAY DIFFRACTION3MYCNSLIB:WATER.PARAMMYCNSLIB:NFW.TOP
X-RAY DIFFRACTION4MYCNSLIB:PATCHES.PARAMION.TOP
X-RAY DIFFRACTION5MYCNSLIB:NFW.PARAM

+
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