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- PDB-5nbm: Crystal structure of the Arp4-N-actin(ATP-state) heterodimer boun... -

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Basic information

Entry
Database: PDB / ID: 5nbm
TitleCrystal structure of the Arp4-N-actin(ATP-state) heterodimer bound by a nanobody
Components
  • Actin
  • Actin-related protein 4
  • Unknown peptide
  • nAct-Nanobody
KeywordsHYDROLASE / Chromatin remodeling / Nanobody / INO80 / SWR1 / NuA4
Function / homology
Function and homology information


RHOB GTPase cycle / RHOA GTPase cycle / cellular bud neck contractile ring / ascospore wall assembly / vacuole inheritance / actin cortical patch / mitotic actomyosin contractile ring contraction / Swr1 complex / kinetochore assembly / Ino80 complex ...RHOB GTPase cycle / RHOA GTPase cycle / cellular bud neck contractile ring / ascospore wall assembly / vacuole inheritance / actin cortical patch / mitotic actomyosin contractile ring contraction / Swr1 complex / kinetochore assembly / Ino80 complex / SWI/SNF complex / establishment of cell polarity / NuA4 histone acetyltransferase complex / actin filament bundle / protein secretion / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / endocytosis / chromatin organization / histone binding / hydrolase activity / chromatin remodeling / DNA repair / DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / ATP binding / identical protein binding / nucleus
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
ADENOSINE-5'-TRIPHOSPHATE / Actin / Actin-related protein 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Vicugna pacos (alpaca)
Trichoplusia ni (cabbage looper)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.4 Å
AuthorsKnoll, K.R. / Eustermann, S. / Hopfner, K.P.
Funding support3items
OrganizationGrant numberCountry
German Research FoundationGRK1721
German Research FoundationCRC1064
European Research CouncilATMMACHINE
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: The nuclear actin-containing Arp8 module is a linker DNA sensor driving INO80 chromatin remodeling.
Authors: Knoll, K.R. / Eustermann, S. / Niebauer, V. / Oberbeckmann, E. / Stoehr, G. / Schall, K. / Tosi, A. / Schwarz, M. / Buchfellner, A. / Korber, P. / Hopfner, K.P.
History
DepositionMar 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actin-related protein 4
B: Actin-related protein 4
C: Actin
D: Actin
E: nAct-Nanobody
F: nAct-Nanobody
G: Unknown peptide
H: Unknown peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,72516
Polymers230,5368
Non-polymers2,1898
Water00
1
A: Actin-related protein 4
D: Actin
F: nAct-Nanobody
G: Unknown peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,3628
Polymers115,2684
Non-polymers1,0954
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Actin-related protein 4
C: Actin
E: nAct-Nanobody
H: Unknown peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,3628
Polymers115,2684
Non-polymers1,0954
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)190.581, 190.581, 220.616
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 15:50 or resseq 52:312 or resseq 382:479))
21(chain B and (resseq 15:50 or resseq 52:312 or resseq 382:479))
12(chain E and resseq 4:126)
22(chain F and resseq 4:126)
13chain C
23chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 15:50 or resseq 52:312 or resseq 382:479))A15 - 50
121(chain A and (resseq 15:50 or resseq 52:312 or resseq 382:479))A52 - 312
131(chain A and (resseq 15:50 or resseq 52:312 or resseq 382:479))A382 - 479
211(chain B and (resseq 15:50 or resseq 52:312 or resseq 382:479))B15 - 50
221(chain B and (resseq 15:50 or resseq 52:312 or resseq 382:479))B52 - 312
231(chain B and (resseq 15:50 or resseq 52:312 or resseq 382:479))B382 - 479
112(chain E and resseq 4:126)E4 - 126
212(chain F and resseq 4:126)F4 - 126
113chain CC2 - 374
213chain DD2 - 374

NCS ensembles :
ID
1
2
3

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Actin-related protein 4 / Actin-like protein ARP4 / Actin-like protein 4


Mass: 54894.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Actin-related protein 4 (ATP bound)
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: ARP4, ACT3, YJL081C, J1012 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P80428
#2: Protein Actin


Mass: 41748.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Actin (ATP bound)
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: ACT1, ABY1, END7, YFL039C / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P60010

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Antibody / Protein/peptide , 2 types, 4 molecules EFGH

#3: Antibody nAct-Nanobody


Mass: 17159.881 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-actin and Arp4 binding nanobody with a C-terminal double Strep-Tag.
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#4: Protein/peptide Unknown peptide


Mass: 1464.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: We could not assign any amino acid sequence of our recombinantly expressed proteins to the electron density maps.
Source: (gene. exp.) Trichoplusia ni (cabbage looper) / Production host: Trichoplusia ni (cabbage looper)

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Non-polymers , 2 types, 8 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 5.02 Å3/Da / Density % sol: 75.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1 mM ATP, 0.2 mM CaCl2, 1.3-1.5 M sodium malonate pH 6.0, Subtilisin (1/6000; w(subtilisin)/w(protein))

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→49.23 Å / Num. obs: 62339 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 93.01 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.07 / Rrim(I) all: 0.18 / Net I/σ(I): 11.3 / Num. measured all: 405414 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
3.4-3.496.81.1130.6960.4631.206100
15.21-49.235.90.0360.9990.0160.0496.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.58 Å47.73 Å
Translation5.58 Å47.73 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimless0.5.25data scaling
PHASER2.6.1phasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→47.735 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.12
RfactorNum. reflection% reflection
Rfree0.193 3124 5.02 %
Rwork0.1519 --
obs0.1539 62264 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 204.21 Å2 / Biso mean: 92.2412 Å2 / Biso min: 36.86 Å2
Refinement stepCycle: final / Resolution: 3.4→47.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13949 0 152 0 14101
Biso mean--86.82 --
Num. residues----1803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314385
X-RAY DIFFRACTIONf_angle_d0.65919547
X-RAY DIFFRACTIONf_chiral_restr0.0452177
X-RAY DIFFRACTIONf_plane_restr0.0042497
X-RAY DIFFRACTIONf_dihedral_angle_d11.438579
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3792X-RAY DIFFRACTION4.425TORSIONAL
12B3792X-RAY DIFFRACTION4.425TORSIONAL
21E1150X-RAY DIFFRACTION4.425TORSIONAL
22F1150X-RAY DIFFRACTION4.425TORSIONAL
31C3535X-RAY DIFFRACTION4.425TORSIONAL
32D3535X-RAY DIFFRACTION4.425TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4001-3.45320.30261570.23826592816100
3.4532-3.50980.2661460.227326872833100
3.5098-3.57030.26551120.217326882800100
3.5703-3.63520.27021380.207626822820100
3.6352-3.70510.25981360.203826882824100
3.7051-3.78070.24121500.195226992849100
3.7807-3.86290.21511420.187826472789100
3.8629-3.95270.22221470.165126682815100
3.9527-4.05150.22321260.15527342860100
4.0515-4.1610.17471870.135826422829100
4.161-4.28340.15491520.12426522804100
4.2834-4.42150.14751360.11627062842100
4.4215-4.57950.18091470.122126642811100
4.5795-4.76260.17561450.124426952840100
4.7626-4.97920.16361180.126227032821100
4.9792-5.24140.17291380.127127112849100
5.2414-5.56930.20091360.143126792815100
5.5693-5.99860.20031410.15327022843100
5.9986-6.60080.19271320.157427112843100
6.6008-7.55270.20561350.158827062841100
7.5527-9.50330.14881620.128726922854100
9.5033-47.73950.18251410.15722725286699
Refinement TLS params.Method: refined / Origin x: -36.4562 Å / Origin y: 201.6636 Å / Origin z: 27.9626 Å
111213212223313233
T0.4617 Å2-0.0773 Å2-0.0416 Å2-0.5655 Å20.0607 Å2--0.475 Å2
L0.6923 °2-0.0826 °2-0.0518 °2-0.7443 °20.0729 °2--1.1629 °2
S-0.0553 Å °-0.0516 Å °-0.0176 Å °-0.0534 Å °0.014 Å °0.0381 Å °0.2376 Å °-0.4208 Å °0.0409 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA15 - 479
2X-RAY DIFFRACTION1allA501 - 502
3X-RAY DIFFRACTION1allB15 - 479
4X-RAY DIFFRACTION1allB501 - 502
5X-RAY DIFFRACTION1allC2 - 374
6X-RAY DIFFRACTION1allC501 - 502
7X-RAY DIFFRACTION1allD2 - 374
8X-RAY DIFFRACTION1allD501 - 502
9X-RAY DIFFRACTION1allE3 - 126
10X-RAY DIFFRACTION1allF3 - 126
11X-RAY DIFFRACTION1allG1 - 17
12X-RAY DIFFRACTION1allH1 - 16

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