[English] 日本語
Yorodumi
- PDB-4yc7: Crystal structure of human FMNL2 GBD-FH3 Domains bound to Cdc42-GppNHp -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yc7
TitleCrystal structure of human FMNL2 GBD-FH3 Domains bound to Cdc42-GppNHp
Components
  • Cell division control protein 42 homolog
  • Formin-like protein 2
KeywordsSIGNALING PROTEIN / Armadillo repeat / Rho GTPase / cell cycle
Function / homology
Function and homology information


small GTPase binding => GO:0031267 / GBD domain binding / submandibular salivary gland formation / actin filament branching / Golgi transport complex / positive regulation of pinocytosis / modification of synaptic structure / endothelin receptor signaling pathway involved in heart process / Cdc42 protein signal transduction / cardiac neural crest cell migration involved in outflow tract morphogenesis ...small GTPase binding => GO:0031267 / GBD domain binding / submandibular salivary gland formation / actin filament branching / Golgi transport complex / positive regulation of pinocytosis / modification of synaptic structure / endothelin receptor signaling pathway involved in heart process / Cdc42 protein signal transduction / cardiac neural crest cell migration involved in outflow tract morphogenesis / positive regulation of synapse structural plasticity / dendritic cell migration / storage vacuole / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / neuron fate determination / modulation by host of viral process / GTP-dependent protein binding / organelle transport along microtubule / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / Inactivation of CDC42 and RAC1 / cardiac conduction system development / regulation of filopodium assembly / establishment of Golgi localization / leading edge membrane / neuropilin signaling pathway / positive regulation of intracellular protein transport / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / regulation of modification of postsynaptic structure / mitogen-activated protein kinase kinase kinase binding / dendritic spine morphogenesis / thioesterase binding / embryonic heart tube development / regulation of stress fiber assembly / regulation of cell morphogenesis / RHO GTPases activate KTN1 / regulation of lamellipodium assembly / nuclear migration / DCC mediated attractive signaling / adherens junction organization / sprouting angiogenesis / Wnt signaling pathway, planar cell polarity pathway / CD28 dependent Vav1 pathway / regulation of postsynapse organization / positive regulation of filopodium assembly / cortical actin cytoskeleton organization / regulation of mitotic nuclear division / phagocytosis, engulfment / RHOV GTPase cycle / establishment or maintenance of cell polarity / heart contraction / Myogenesis / RHOJ GTPase cycle / Golgi organization / RHOQ GTPase cycle / positive regulation of cytokinesis / RHO GTPases activate PAKs / CDC42 GTPase cycle / RHOU GTPase cycle / macrophage differentiation / RHOG GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC2 GTPase cycle / RHO GTPases activate IQGAPs / RAC3 GTPase cycle / spindle midzone / negative regulation of protein-containing complex assembly / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / phagocytic vesicle / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / cytoskeleton organization / RAC1 GTPase cycle / EPHB-mediated forward signaling / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / small monomeric GTPase / G protein activity / secretory granule / positive regulation of DNA replication / filopodium / integrin-mediated signaling pathway / RHO GTPases Activate Formins / actin filament organization / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / EGFR downregulation / positive regulation of JNK cascade / MAPK6/MAPK4 signaling / Schaffer collateral - CA1 synapse / protein localization / G beta:gamma signalling through CDC42 / mitotic spindle / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / cellular response to type II interferon
Similarity search - Function
Formin-like protein 2 / Formin-like protein, animal / Diaphanous autoregulatory (DAD) domain / Diaphanous autoregulatory domain (DAD) profile. / Cdc42 / Formin, FH3 domain / Formin, GTPase-binding domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Diaphanous FH3 Domain ...Formin-like protein 2 / Formin-like protein, animal / Diaphanous autoregulatory (DAD) domain / Diaphanous autoregulatory domain (DAD) profile. / Cdc42 / Formin, FH3 domain / Formin, GTPase-binding domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain profile. / Formin, FH2 domain / Formin, FH2 domain superfamily / Formin Homology 2 Domain / Formin homology-2 (FH2) domain profile. / Formin Homology 2 Domain / Small GTPase Rho / small GTPase Rho family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Cell division control protein 42 homolog / Formin-like protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKuhn, S. / Geyer, M.
CitationJournal: Nat Commun / Year: 2015
Title: The structure of FMNL2-Cdc42 yields insights into the mechanism of lamellipodia and filopodia formation.
Authors: Kuhn, S. / Erdmann, C. / Kage, F. / Block, J. / Schwenkmezger, L. / Steffen, A. / Rottner, K. / Geyer, M.
History
DepositionFeb 19, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Formin-like protein 2
A: Cell division control protein 42 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6564
Polymers64,1092
Non-polymers5472
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-19 kcal/mol
Surface area22520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.094, 91.094, 144.275
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Formin-like protein 2 / Formin homology 2 domain-containing protein 2 / FMNL2


Mass: 44081.191 Da / Num. of mol.: 1 / Fragment: UNP residues 1-379
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FMNL2, FHOD2, KIAA1902 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96PY5
#2: Protein Cell division control protein 42 homolog / G25K GTP-binding protein / Cdc42


Mass: 20027.961 Da / Num. of mol.: 1 / Fragment: UNP residues 1-179
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC42 / Production host: Escherichia coli (E. coli) / References: UniProt: P60953
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20 mM Tris/HCl (pH 8.0), 14% (v/v) PEG 3350, 0.25 M magnesium acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→43.4 Å / Num. obs: 22213 / % possible obs: 100 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 25.9
Reflection shellHighest resolution: 2.5 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 4.4 / Num. measured obs: 4521 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.3_928)refinement
PHENIXphasing
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB accession code 3EG5, Chain A

3eg5


Resolution: 2.5→43.4 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 22.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2534 1110 5.12 %
Rwork0.1935 --
obs0.1964 21696 99.99 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.781 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.1795 Å20 Å20 Å2
2--2.1795 Å20 Å2
3---2.6871 Å2
Refinement stepCycle: LAST / Resolution: 2.5→43.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3807 0 33 63 3903
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083911
X-RAY DIFFRACTIONf_angle_d1.1335296
X-RAY DIFFRACTIONf_dihedral_angle_d16.5551480
X-RAY DIFFRACTIONf_chiral_restr0.083598
X-RAY DIFFRACTIONf_plane_restr0.004677
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5002-2.6140.40471440.3682520X-RAY DIFFRACTION100
2.614-2.75180.38341340.34672515X-RAY DIFFRACTION100
2.7518-2.92410.30971340.25862518X-RAY DIFFRACTION100
2.9241-3.14980.30731550.23392518X-RAY DIFFRACTION100
3.1498-3.46670.25561460.18752549X-RAY DIFFRACTION100
3.4667-3.96810.27021270.18032586X-RAY DIFFRACTION100
3.9681-4.99820.1891180.14762624X-RAY DIFFRACTION100
4.9982-43.44050.2251520.17732756X-RAY DIFFRACTION100
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)
11.0179-0.2645-0.07550.43720.27970.56850.3604-0.2526-0.59710.52370.1933-0.62180.80220.56210.00050.6968-0.0414-0.11190.69220.06440.450519.11749.0769-14.9933
21.43220.9878-0.60361.77790.02681.2092-0.14240.243-0.1281-0.20710.09390.00290.2306-0.0313-0.00020.3260.03960.08040.4552-0.06840.381411.862111.4267-46.214
30.98041.2436-0.57621.58270.08630.5553-0.14190.2447-0.0208-0.16620.09730.1032-0.10730.2191-00.27510.0051-0.01660.41850.00520.319419.985929.8387-42.2741
40.44420.59130.43640.55360.44660.58510.22760.16330.9214-0.03410.03780.0268-0.45990.45220.00020.53-0.05840.04940.44720.10650.560123.605846.5485-38.4926
50.8661-0.6803-0.19260.51210.05510.0793-0.07680.0095-0.14840.4669-0.009-0.2081-0.12640.15710.00010.3174-0.03840.00060.4542-0.05970.24750.849120.2109-10.6491
60.1797-0.0964-0.17410.3386-0.10650.2335-0.3016-0.7533-0.18810.0858-0.0529-0.2403-0.0010.4198-0.00010.39260.00050.03350.54670.06260.3881-4.170310.6294-8.8145
70.3015-0.26430.00170.29460.13960.40370.01660.2773-0.29460.6005-0.0199-0.2352-0.17480.1434-0.00020.40.0237-0.00830.5192-0.00190.43039.842813.6475-20.3581
80.29080.2605-0.09180.40160.33290.3225-0.0669-0.09790.1998-0.2490.1727-0.2067-0.08470.116-0.00010.30490.02470.03960.4989-0.03480.42291.657321.1847-26.5547
91.13370.3643-0.41760.2318-0.37020.49270.35280.10550.1767-0.024-0.40290.458-0.0296-0.4656-0.00370.38990.06710.09480.4896-0.05250.4639-3.107830.494-21.783
100.1039-0.0274-0.01960.1726-0.27490.3564-0.11220.3040.4517-0.9953-0.2560.5838-0.0183-0.0038-0.00010.41520.098-0.04720.56870.01940.582-6.77730.7928-30.2499
110.0647-0.08070.0160.2244-0.20460.206-0.1424-0.08150.59230.1533-0.170.7218-0.2435-0.3499-0.0030.3388-0.04460.08740.4714-0.15080.4912-9.180424.5851-18.8619
120.4480.84470.48242.68792.30362.1408-0.30350.09810.5532-0.7623-0.40311.0664-1.0165-0.2774-0.08180.2491-0.07490.20460.6944-0.11670.5371-12.053215.0099-15.7053
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resseq 32:75)
2X-RAY DIFFRACTION2chain 'B' and (resseq 76:219)
3X-RAY DIFFRACTION3chain 'B' and (resseq 220:329)
4X-RAY DIFFRACTION4chain 'B' and (resseq 330:377)
5X-RAY DIFFRACTION5chain 'A' and (resseq -1:36)
6X-RAY DIFFRACTION6chain 'A' and (resseq 37:58)
7X-RAY DIFFRACTION7chain 'A' and (resseq 59:76)
8X-RAY DIFFRACTION8chain 'A' and (resseq 77:104)
9X-RAY DIFFRACTION9chain 'A' and (resseq 105:131)
10X-RAY DIFFRACTION10chain 'A' and (resseq 132:148)
11X-RAY DIFFRACTION11chain 'A' and (resseq 149:164)
12X-RAY DIFFRACTION12chain 'A' and (resseq 165:177)

+
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