[English] 日本語
Yorodumi
- PDB-1waa: IG27 protein domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1waa
TitleIG27 protein domain
Components(TITIN) x 3
KeywordsMETAL BINDING PROTEIN / CALMODULIN-BINDING / CYTOSKELETON / IMMUNOGLOBULIN DOMAIN / MUSCLE PROTEIN / PHOSPHORYLATION / SERINE/THREONINE- PROTEIN KINASE / STRUCTURAL PROTEIN.
Function / homology
Function and homology information


sarcomerogenesis / titin-telethonin complex / structural molecule activity conferring elasticity / skeletal muscle myosin thick filament assembly / telethonin binding / detection of muscle stretch / muscle alpha-actinin binding / : / cardiac myofibril assembly / cardiac muscle hypertrophy ...sarcomerogenesis / titin-telethonin complex / structural molecule activity conferring elasticity / skeletal muscle myosin thick filament assembly / telethonin binding / detection of muscle stretch / muscle alpha-actinin binding / : / cardiac myofibril assembly / cardiac muscle hypertrophy / mitotic chromosome condensation / cardiac muscle tissue morphogenesis / Striated Muscle Contraction / muscle filament sliding / protein kinase regulator activity / actinin binding / M band / I band / cardiac muscle cell development / structural constituent of muscle / sarcomere organization / striated muscle thin filament / skeletal muscle thin filament assembly / skeletal muscle contraction / striated muscle contraction / cardiac muscle contraction / muscle contraction / condensed nuclear chromosome / positive regulation of protein secretion / response to calcium ion / Z disc / actin filament binding / Platelet degranulation / protease binding / protein tyrosine kinase activity / calmodulin binding / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / calcium ion binding / positive regulation of gene expression / protein kinase binding / enzyme binding / protein homodimerization activity / extracellular exosome / extracellular region / ATP binding / identical protein binding / cytosol
Similarity search - Function
PPAK motif / PPAK motif / Titin, Z repeat / Titin Z / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain ...PPAK motif / PPAK motif / Titin, Z repeat / Titin Z / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase domain / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsVega, M.C. / Valencia, L. / Zou, P. / Wilmanns, M.
CitationJournal: Plos Comput.Biol. / Year: 2009
Title: Mechanical Network in Titin Immunoglobulin from Force Distribution Analysis.
Authors: Stacklies, W. / Vega, M.C. / Wilmanns, M. / Grater, F.
History
DepositionOct 25, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2006Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2Jul 24, 2019Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _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: TITIN
B: TITIN
C: TITIN
D: TITIN
E: TITIN
F: TITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,34530
Polymers60,7766
Non-polymers1,57024
Water8,647480
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10740 Å2
ΔGint-757.7 kcal/mol
Surface area24860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.240, 75.990, 134.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
TITIN / I27 DOMAIN FROM TITIN / HEART ISOFORM N2-B


Mass: 10124.597 Da / Num. of mol.: 4 / Fragment: IG DOMAIN, RESIDUES 12801-12889
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: MUSCLE / Organ: HEART / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q8WZ42, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Protein TITIN / I27 DOMAIN FROM TITIN / HEART ISOFORM N2-B


Mass: 10138.623 Da / Num. of mol.: 1 / Fragment: IG DOMAIN, RESIDUES 12801-12889
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: MUSCLE / Organ: HEART / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q8WZ42, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#3: Protein TITIN / I27 DOMAIN FROM TITIN / HEART ISOFORM N2-B


Mass: 10138.622 Da / Num. of mol.: 1 / Fragment: IG DOMAIN, RESIDUES 12801-12889
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: MUSCLE / Organ: HEART / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q8WZ42, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#4: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: THIS MUSCLE PROTEIN MAY BE INVOLVED IN MUSCLE ASSEMBLY AND MAINTAINING THE STRUCTURAL ...FUNCTION: THIS MUSCLE PROTEIN MAY BE INVOLVED IN MUSCLE ASSEMBLY AND MAINTAINING THE STRUCTURAL INTEGRITY OF SARCOMERES

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.9 %

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.84
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.84 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 53298 / % possible obs: 89.2 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.3
Reflection shellResolution: 1.8→2 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 5.4 / % possible all: 92.3

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TIT

1tit


Resolution: 1.8→15 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.904 / SU B: 13.244 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.268 3714 7.2 %RANDOM
Rwork0.207 ---
obs0.211 47862 86.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2---0.12 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4215 0 24 480 4719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224189
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.9645648
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7935546
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.2726.604159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.5115713
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1210.2649
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023058
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.260.21879
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.22778
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2348
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.28722793
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.09434344
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8674.51542
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.80261304
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: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.2 1
Rwork0.231 4055
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)
12.89351.9134-0.55136.1637-1.47981.6813-0.00970.0622-0.0367-0.21540.00990.04170.1178-0.0163-0.0001-0.150.0115-0.0171-0.13960.0097-0.114151.531738.814692.6619
23.1817-0.00722.24251.1946-0.89155.999-0.01310.22450.1673-0.05210.0123-0.0768-0.20730.1340.0008-0.10860.01490.0115-0.0952-0.0129-0.129751.116166.182571.003
32.39462.39850.97186.84931.45161.7958-0.09150.07850.1393-0.23460.00960.1335-0.1137-0.03560.0819-0.11970.005-0.0112-0.1228-0.0099-0.092742.818578.648889.9914
44.1636-0.5316-2.2542.3610.96244.7045-0.02570.1826-0.2281-0.09550.02040.03540.2656-0.07490.0053-0.11450.0205-0.0341-0.0989-0.0293-0.116243.192748.752172.4666
54.925-2.94382.27724.7246-1.94854.8237-0.1037-0.3677-0.11240.48660.20790.1890.2061-0.013-0.1042-0.01780.00040.0238-0.06320.0228-0.097642.752248.8668106.4446
63.7266-2.2217-1.73654.12352.37713.4532-0.0621-0.272-0.09650.2530.0397-0.00120.0595-0.05150.0224-0.1123-0.001-0.0227-0.0628-0.0184-0.120651.211971.0214105.3923
70.271-0.02150.02650.69060.00630.2749-0.0126-0.0071-0.00170.0097-0.0150.00010.00830.01610.02770.01620.0079-0.00270.0369-0.0110.034147.936258.437388.8532
80.6215-0.3057-0.16650.92720.02461.2811-0.0604-0.0563-0.06980.01750.02790.03560.1835-0.03470.0324-0.08550.0053-0.0222-0.0537-0.0134-0.027546.268457.073589.7216
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 89
2X-RAY DIFFRACTION2B1 - 89
3X-RAY DIFFRACTION3C-2 - 89
4X-RAY DIFFRACTION4D-3 - 89
5X-RAY DIFFRACTION5E-3 - 89
6X-RAY DIFFRACTION6F-3 - 89
7X-RAY DIFFRACTION7A2001 - 2105
8X-RAY DIFFRACTION7B2001 - 2088
9X-RAY DIFFRACTION7C2001 - 2075
10X-RAY DIFFRACTION7D2001 - 2073
11X-RAY DIFFRACTION7E2001 - 2062
12X-RAY DIFFRACTION7F2001 - 2077
13X-RAY DIFFRACTION8A1090 - 1094
14X-RAY DIFFRACTION8B1090 - 1094
15X-RAY DIFFRACTION8C1090 - 1094
16X-RAY DIFFRACTION8D1090 - 1092
17X-RAY DIFFRACTION8E1089 - 1091
18X-RAY DIFFRACTION8F1090 - 1092

+
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