[English] 日本語
Yorodumi
- PDB-3rbw: Crystal structure of Spire KIND domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rbw
TitleCrystal structure of Spire KIND domain
ComponentsProtein spire homolog 1
KeywordsPROTEIN BINDING / C-lobe of protein kinases / actin nucleator / Fmn-family formins
Function / homology
Function and homology information


formin-nucleated actin cable assembly / establishment of meiotic spindle localization / polar body extrusion after meiotic divisions / actin filament network formation / actin nucleation / Golgi vesicle transport / cleavage furrow formation / positive regulation of mitochondrial fission / positive regulation of double-strand break repair / intracellular transport ...formin-nucleated actin cable assembly / establishment of meiotic spindle localization / polar body extrusion after meiotic divisions / actin filament network formation / actin nucleation / Golgi vesicle transport / cleavage furrow formation / positive regulation of mitochondrial fission / positive regulation of double-strand break repair / intracellular transport / vesicle-mediated transport / cytoplasmic vesicle membrane / protein transport / actin binding / actin cytoskeleton organization / cell cortex / microtubule binding / mitochondrial outer membrane / cytoskeleton / innate immune response / perinuclear region of cytoplasm / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
Protein Spire1 / Protein Spire / Kinase non-catalytic C-lobe domain / KIND domain / KIND domain profile. / kinase non-catalytic C-lobe domain / Zinc finger, FYVE/PHD-type / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein spire homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsVizcarra, C.L. / Kreutz, B. / Rodal, A.A. / Toms, A.V. / Lu, J. / Zheng, W. / Quinlan, M.E. / Eck, M.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structure of the Spire KIND domain and insights into its interaction with Fmn-family formins
Authors: Vizcarra, C. / Kreutz, B. / Rodal, A. / Toms, A. / Lu, J. / Zheng, W. / Quinlan, M. / Eck, M.
History
DepositionMar 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein spire homolog 1
B: Protein spire homolog 1
C: Protein spire homolog 1
D: Protein spire homolog 1


Theoretical massNumber of molelcules
Total (without water)96,1114
Polymers96,1114
Non-polymers00
Water905
1
A: Protein spire homolog 1


Theoretical massNumber of molelcules
Total (without water)24,0281
Polymers24,0281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein spire homolog 1


Theoretical massNumber of molelcules
Total (without water)24,0281
Polymers24,0281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein spire homolog 1


Theoretical massNumber of molelcules
Total (without water)24,0281
Polymers24,0281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protein spire homolog 1


Theoretical massNumber of molelcules
Total (without water)24,0281
Polymers24,0281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.328, 66.265, 100.852
Angle α, β, γ (deg.)90.00, 103.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13A
23B
33C
43D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A37 - 231
2112B37 - 231
1122C37 - 231
2122D37 - 231
1132A99 - 103
2132B99 - 103
3132C99 - 103
4132D99 - 103
1232A76 - 80
2232B76 - 80
3232C76 - 80
4232D76 - 80
1332A83 - 87
2332B83 - 87
3332C83 - 87
4332D83 - 87
1432A140 - 145
2432B140 - 145
3432C140 - 145
4432D140 - 145
1532A206 - 210
2532B206 - 210
3532C206 - 210
4532D206 - 210

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein
Protein spire homolog 1 / Spir-1


Mass: 24027.785 Da / Num. of mol.: 4 / Fragment: KIND domain (UNP residues 20-237)
Source method: isolated from a genetically manipulated source
Details: Spir1 KIND 20-237 / Source: (gene. exp.) Homo sapiens (human) / Gene: SPIRE1, KIAA1135, SPIR1 / Plasmid: pET HisTT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q08AE8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.48 Å3/Da / Density % sol: 50.48 %
Crystal growMethod: vapor diffusion / Details: VAPOR DIFFUSION

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 4, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.2→41 Å / Num. obs: 14983 / % possible obs: 94.3 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 14

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3r7g

3r7g


Resolution: 3.2→25 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.908 / SU B: 67.651 / SU ML: 0.504 / Cross valid method: THROUGHOUT / ESU R Free: 0.613 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.31501 743 5 %RANDOM
Rwork0.2606 ---
obs0.26325 14116 94.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 99.679 Å2
Baniso -1Baniso -2Baniso -3
1--6.58 Å20 Å21.69 Å2
2---6.72 Å20 Å2
3---14.06 Å2
Refinement stepCycle: LAST / Resolution: 3.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4845 0 0 5 4850
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0214924
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3321.9616660
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9315596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.42423.241253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.615859
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9871558
X-RAY DIFFRACTIONr_chiral_restr0.0860.2740
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213760
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4551.53040
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.77724865
X-RAY DIFFRACTIONr_scbond_it4.42931884
X-RAY DIFFRACTIONr_scangle_it7.7944.51795
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A612TIGHT POSITIONAL0.030.05
1A603MEDIUM POSITIONAL0.040.5
1A612TIGHT THERMAL0.070.5
1A603MEDIUM THERMAL0.082
2C596TIGHT POSITIONAL0.020.05
2C594MEDIUM POSITIONAL0.030.5
2C596TIGHT THERMAL0.030.5
2C594MEDIUM THERMAL0.032
3A96TIGHT POSITIONAL0.040.05
3B96TIGHT POSITIONAL0.030.05
3C96TIGHT POSITIONAL0.030.05
3D96TIGHT POSITIONAL0.040.05
3A93MEDIUM POSITIONAL0.030.5
3B93MEDIUM POSITIONAL0.030.5
3C93MEDIUM POSITIONAL0.030.5
3D93MEDIUM POSITIONAL0.030.5
3A96TIGHT THERMAL0.590.5
3B96TIGHT THERMAL0.580.5
3C96TIGHT THERMAL0.580.5
3D96TIGHT THERMAL0.590.5
3A93MEDIUM THERMAL0.082
3B93MEDIUM THERMAL0.072
3C93MEDIUM THERMAL0.082
3D93MEDIUM THERMAL0.082
LS refinement shellResolution: 3.2→3.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 54 -
Rwork0.383 882 -
obs--82.39 %
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)
11.59971.61170.74918.5237-0.60921.49290.03810.3535-0.1161-0.16330.1519-0.0069-0.28330.1036-0.190.4174-0.0760.11320.5121-0.02750.046722.8569-6.316642.3809
21.18970.17520.43952.79250.64012.1374-0.0123-0.0501-0.08440.2754-0.02210.3756-0.06420.06060.03450.4706-0.00450.14750.3524-0.0020.10118.7881-8.984352.2519
32.27970.9746-0.21385.58290.42540.80810.050.2734-0.0134-0.27280.124-0.1024-0.27020.0874-0.1740.404-0.0957-0.11730.39950.00430.532-2.5938-4.2375-6.7076
41.40360.42840.60432.35770.37532.48520.0281-0.00190.16490.2674-0.07410.1913-0.0484-0.01210.0460.35610.0265-0.06050.24260.00350.6839-6.5192-6.94773.1695
55.28820.2412-0.5993.29070.07362.0966-0.05180.530.1379-0.0593-0.09080.1358-0.25250.10440.14260.3863-0.08990.0540.41240.02620.3454-18.6022-21.047936.7879
68.47411.6798-1.88343.6496-0.48452.76080.0055-1.4446-0.455-0.1584-0.4313-0.1839-0.31130.22510.42580.24720.08280.00850.5190.01210.6176-29.221614.09912.5887
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 131
2X-RAY DIFFRACTION2A132 - 232
3X-RAY DIFFRACTION3B38 - 131
4X-RAY DIFFRACTION4B132 - 232
5X-RAY DIFFRACTION5C37 - 232
6X-RAY DIFFRACTION6D37 - 231

+
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