[English] 日本語
Yorodumi
- PDB-2v01: Recombinant vertebrate calmodulin complexed with Pb -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2v01
TitleRecombinant vertebrate calmodulin complexed with Pb
ComponentsCALMODULIN
KeywordsMETAL BINDING PROTEIN / METHYLATION / PHOSPHORYLATION / METAL-BINDING PROTEIN
Function / homology
Function and homology information


: / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / CaM pathway / response to corticosterone / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor ...: / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / CaM pathway / response to corticosterone / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / regulation of synaptic vesicle endocytosis / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / PKA activation / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / regulation of synaptic vesicle exocytosis / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / autophagosome membrane docking / Negative regulation of NMDA receptor-mediated neuronal transmission / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / Unblocking of NMDA receptors, glutamate binding and activation / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Phase 0 - rapid depolarisation / protein phosphatase activator activity / RHO GTPases activate PAKs / positive regulation of cyclic-nucleotide phosphodiesterase activity / Long-term potentiation / positive regulation of phosphoprotein phosphatase activity / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / adenylate cyclase binding / catalytic complex / detection of calcium ion / DARPP-32 events / Smooth Muscle Contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / RHO GTPases activate IQGAPs / cellular response to interferon-beta / regulation of cardiac muscle contraction / calcium channel inhibitor activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / positive regulation of DNA binding / Protein methylation / enzyme regulator activity / voltage-gated potassium channel complex / Activation of AMPK downstream of NMDARs / phosphatidylinositol 3-kinase binding / eNOS activation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / response to amphetamine / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Ion homeostasis / positive regulation of protein autophosphorylation / sperm midpiece / calcium channel complex / activation of adenylate cyclase activity / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / protein serine/threonine kinase activator activity / regulation of heart rate / nitric-oxide synthase regulator activity / sarcomere / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / regulation of cytokinesis / VEGFR2 mediated cell proliferation / positive regulation of nitric-oxide synthase activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / spindle microtubule / mitochondrial membrane / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of protein serine/threonine kinase activity / Transcriptional activation of mitochondrial biogenesis / synaptic vesicle membrane / cellular response to type II interferon / Stimuli-sensing channels / spindle pole / response to calcium ion
Similarity search - Function
EF-hand / Recoverin; domain 1 / EF-hand domain pair / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
LEAD (II) ION / Calmodulin-1 / Calmodulin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsKursula, P. / Majava, V.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2007
Title: A Structural Insight Into Lead Neurotoxicity and Calmodulin Activation by Heavy Metals.
Authors: Kursula, P. / Majava, V.
History
DepositionMay 4, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Mar 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,55010
Polymers16,8531
Non-polymers1,6989
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)24.580, 29.950, 53.610
Angle α, β, γ (deg.)88.57, 87.03, 82.95
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein CALMODULIN / / CAM


Mass: 16852.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PETCM / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLySS / References: UniProt: P62158, UniProt: P0DP23*PLUS
#2: Chemical
ChemComp-PB / LEAD (II) ION / Lead


Mass: 207.200 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Pb
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.37 Å3/Da / Density % sol: 47.72 % / Description: NONE
Crystal growpH: 4 / Details: 40-50%MPD, PH4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0408
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0408 Å / Relative weight: 1
ReflectionResolution: 2.15→20 Å / Num. obs: 7838 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Biso Wilson estimate: 31.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.2
Reflection shellResolution: 2.15→2.25 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 4.3 / % possible all: 90.2

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UP5
Resolution: 2.15→20 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.892 / SU B: 11.876 / SU ML: 0.154 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.253 392 5 %RANDOM
Rwork0.188 ---
obs0.191 7837 95.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å2-0.85 Å2-0.98 Å2
2--2.46 Å22.69 Å2
3----1.63 Å2
Refinement stepCycle: LAST / Resolution: 2.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1114 0 9 55 1178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221138
X-RAY DIFFRACTIONr_bond_other_d0.0010.02754
X-RAY DIFFRACTIONr_angle_refined_deg1.2981.9631511
X-RAY DIFFRACTIONr_angle_other_deg0.88231846
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5015140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.64226.46265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.47115212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.027156
X-RAY DIFFRACTIONr_chiral_restr0.0680.2164
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021282
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02212
X-RAY DIFFRACTIONr_nbd_refined0.2280.2333
X-RAY DIFFRACTIONr_nbd_other0.1790.2776
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2583
X-RAY DIFFRACTIONr_nbtor_other0.0850.2575
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.251
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2670.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2850.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4521.5699
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.81621115
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5233457
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2514.5396
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: 2.15→2.21 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.249 25
Rwork0.205 482
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.84058.89122.965713.5565.249327.64131.5309-1.68440.14961.6329-1.1814-1.3046-0.65841.0989-0.3496-0.0368-0.0867-0.03751.01950.0869-0.02915.741413.3764-4.4742
25.76570.7341-0.26436.6182-2.53233.9410.033-0.3603-0.7719-0.40060.04560.21790.372-0.1248-0.0786-0.197-0.0151-0.0477-0.3907-0.0103-0.11645.93164.9838-18.7505
31.77182.6608-3.679514.413-17.686426.9336-0.2705-1.6507-0.41340.53850.48810.04750.2274-1.0925-0.2176-0.076-0.08880.05490.53720.105-0.11474.20648.3062-2.2768
411.91840.7784-4.53513.0145-1.305913.2814-0.1011.59820.5553-0.1180.0103-0.1314-0.09680.2080.0908-0.21160.02470.0164-0.02890.0641-0.2235-7.0499-9.852319.2138
519.75427.1951-0.636614.7868-4.666625.2943-0.07130.89380.3866-0.8413-0.2413-0.1579-0.9244-0.44590.3126-0.1320.10390.0080.38130.0749-0.2137-10.2381-7.72278.9098
60000000000000000.19570.028-0.02080.2106-0.13570.0124-14.474-17.301221.9635
7000000000000000-0.14430.00790.0417-0.3617-0.0679-0.125911.75810.2912-22.1655
8000000000000000-0.0831-0.03120.0035-0.174-0.0002-0.09512.550115.8262-18.1214
90000000000000000.23840.06560.05510.6202-0.04250.1177-3.2381-15.877114.4743
100000000000000000.1072-0.1054-0.03930.8707-0.06540.0167-12.6059-12.58718.6442
110000000000000000.86540.1336-0.02820.33510.17890.65942.280122.3671-18.1734
120000000000000001.1569-0.17620.2451.3124-0.19081.061720.64085.431-5.0641
130000000000000000.51480.02440.08240.22490.11580.56543.782119.2181-15.6193
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 15
2X-RAY DIFFRACTION2A16 - 64
3X-RAY DIFFRACTION3A65 - 85
4X-RAY DIFFRACTION4A86 - 129
5X-RAY DIFFRACTION5A130 - 145
6X-RAY DIFFRACTION6A1146
7X-RAY DIFFRACTION7A1147
8X-RAY DIFFRACTION8A1148
9X-RAY DIFFRACTION9A1149
10X-RAY DIFFRACTION10A1150
11X-RAY DIFFRACTION11A1151
12X-RAY DIFFRACTION12A1152
13X-RAY DIFFRACTION13A1153

+
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