[English] 日本語
Yorodumi
- PDB-4n78: The WAVE Regulatory Complex Links Diverse Receptors to the Actin ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4n78
TitleThe WAVE Regulatory Complex Links Diverse Receptors to the Actin Cytoskeleton
Components
  • Abl interactor 2
  • Cytoplasmic FMR1-interacting protein 1
  • Nck-associated protein 1
  • Protein BRICK1
  • WIRS
  • Wiskott-Aldrich syndrome protein family member 1
KeywordsPROTEIN BINDING / actin dynamics
Function / homology
Function and homology information


peripheral region of growth cone / negative regulation of synaptic vesicle recycling / intracellular protein-containing complex / SCAR complex / zonula adherens assembly / positive regulation of neurotrophin TRK receptor signaling pathway / lamellipodium morphogenesis / positive regulation of Arp2/3 complex-mediated actin nucleation / Arp2/3 complex binding / modification of synaptic structure ...peripheral region of growth cone / negative regulation of synaptic vesicle recycling / intracellular protein-containing complex / SCAR complex / zonula adherens assembly / positive regulation of neurotrophin TRK receptor signaling pathway / lamellipodium morphogenesis / positive regulation of Arp2/3 complex-mediated actin nucleation / Arp2/3 complex binding / modification of synaptic structure / regulation of actin polymerization or depolymerization / central region of growth cone / modification of postsynaptic actin cytoskeleton / dendrite extension / lens fiber cell morphogenesis / regulation of translation at postsynapse, modulating synaptic transmission / filopodium tip / : / regulation of modification of postsynaptic actin cytoskeleton / cytoskeletal anchor activity / regulation of actin filament polymerization / regulation of dendritic spine morphogenesis / RNA 7-methylguanosine cap binding / ruffle organization / actin polymerization or depolymerization / cell projection assembly / axon extension / proline-rich region binding / positive regulation of ruffle assembly / positive regulation of dendrite development / protein kinase A binding / lamellipodium assembly / regulation of myelination / cortical actin cytoskeleton organization / positive regulation of actin filament polymerization / Rac protein signal transduction / protein kinase A regulatory subunit binding / filamentous actin / dendritic growth cone / lamellipodium membrane / excitatory synapse / RHOG GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / RAC2 GTPase cycle / positive regulation of axon extension / signaling adaptor activity / positive regulation of lamellipodium assembly / axonal growth cone / response to electrical stimulus / cytoskeleton organization / translation repressor activity / cellular response to brain-derived neurotrophic factor stimulus / ruffle / RAC1 GTPase cycle / receptor-mediated endocytosis / actin filament polymerization / mitochondrion organization / neuron projection morphogenesis / filopodium / central nervous system development / actin filament organization / cell motility / axon guidance / positive regulation of protein-containing complex assembly / FCGR3A-mediated phagocytosis / adherens junction / cell morphogenesis / terminal bouton / Regulation of actin dynamics for phagocytic cup formation / small GTPase binding / cognition / SH3 domain binding / kinase binding / VEGFA-VEGFR2 Pathway / peptidyl-tyrosine phosphorylation / cellular response to insulin stimulus / specific granule lumen / positive regulation of fibroblast proliferation / actin filament binding / cell migration / actin cytoskeleton / regulation of translation / tertiary granule lumen / lamellipodium / nervous system development / actin binding / regulation of cell shape / fibroblast proliferation / actin cytoskeleton organization / postsynapse / protein-containing complex assembly / secretory granule lumen / in utero embryonic development / mitochondrial outer membrane / dendritic spine / cytoskeleton / neuron projection / focal adhesion / neuronal cell body
Similarity search - Function
Helix Hairpins - #1620 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #150 / ABL interactor 2 / Cytoplasmic FMR1-interacting / Nck-associated protein 1 / Cytoplasmic Fragile-X interacting family / Nck-associated protein 1 / Protein BRICK1 / Abl interactor 2, SH3 domain / CYRIA/CYRIB, Rac1 binding domain ...Helix Hairpins - #1620 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #150 / ABL interactor 2 / Cytoplasmic FMR1-interacting / Nck-associated protein 1 / Cytoplasmic Fragile-X interacting family / Nck-associated protein 1 / Protein BRICK1 / Abl interactor 2, SH3 domain / CYRIA/CYRIB, Rac1 binding domain / Abl-interactor, homeo-domain homologous domain / SCAR/WAVE family / ABI family / CYRIA/CYRIB Rac1 binding domain / Abl-interactor HHR / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / WH2 motif / Wiskott Aldrich syndrome homology region 2 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / WH2 domain / WH2 domain profile. / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Variant SH3 domain / Helix Hairpins / SH3 domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Abl interactor 2 / Cytoplasmic FMR1-interacting protein 1 / Protein BRICK1 / Actin-binding protein WASF1 / Abl interactor 2 / Nck-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsChen, Z.C.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2014
Title: The WAVE Regulatory Complex Links Diverse Receptors to the Actin Cytoskeleton.
Authors: Chen, B. / Brinkmann, K. / Chen, Z. / Pak, C.W. / Liao, Y. / Shi, S. / Henry, L. / Grishin, N.V. / Bogdan, S. / Rosen, M.K.
History
DepositionOct 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Cytoplasmic FMR1-interacting protein 1
B: Nck-associated protein 1
D: Wiskott-Aldrich syndrome protein family member 1
E: Protein BRICK1
F: Abl interactor 2
P: WIRS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)403,90126
Polymers402,2856
Non-polymers1,61520
Water13,439746
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44400 Å2
ΔGint-268 kcal/mol
Surface area111240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.492, 114.750, 323.605
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 5 types, 5 molecules ABDEF

#1: Protein Cytoplasmic FMR1-interacting protein 1 / Specifically Rac1-associated protein 1 / Sra-1 / p140sra-1


Mass: 145363.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYFIP1, KIAA0068 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q7L576
#2: Protein Nck-associated protein 1 / NAP 1 / Membrane-associated protein HEM-2 / p125Nap1


Mass: 128940.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCKAP1, HEM2, KIAA0587, NAP1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9Y2A7
#3: Protein Wiskott-Aldrich syndrome protein family member 1 / WASP family protein member 1 / Protein WAVE-1 / Verprolin homology domain-containing protein 1


Mass: 61728.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WASF1, KIAA0269, SCAR1, WAVE1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92558
#4: Protein Protein BRICK1 / BRK1


Mass: 8756.915 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRK1, C3orf10, HSPC300, MDS027 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WUW1
#5: Protein Abl interactor 2


Mass: 55806.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABI2 / Production host: Escherichia coli (E. coli) / References: UniProt: J3KNB2, UniProt: Q9NYB9*PLUS

-
Protein/peptide , 1 types, 1 molecules P

#6: Protein/peptide WIRS


Mass: 1687.894 Da / Num. of mol.: 1 / Source method: obtained synthetically

-
Non-polymers , 3 types, 766 molecules

#7: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 746 / 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: 2.25 Å3/Da / Density % sol: 45.33 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 8.5
Details: 10% glycerol, 4% PEG 10,000, 12-20% PEG 300, 100 mM Tris-HCl, 2mM EDTA, 2 mM TCEP, pH 8.5, EVAPORATION, temperature 277K

-
Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 12, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.43→20 Å / Num. all: 263711 / Num. obs: 262551 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.43→2.48 Å / % possible all: 99

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→19.977 Å / SU ML: 0.69 / σ(F): 1.34 / Phase error: 24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2089 3512 1.34 %
Rwork0.1891 --
obs0.1894 262551 99.56 %
all-263711 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.526 Å2 / ksol: 0.323 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-16.7148 Å20 Å2-0 Å2
2--0.0943 Å20 Å2
3----16.8091 Å2
Refinement stepCycle: LAST / Resolution: 2.43→19.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21908 0 100 746 22754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00222517
X-RAY DIFFRACTIONf_angle_d0.46330397
X-RAY DIFFRACTIONf_dihedral_angle_d10.9828527
X-RAY DIFFRACTIONf_chiral_restr0.0363417
X-RAY DIFFRACTIONf_plane_restr0.0023871
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.46320.37821350.30969742X-RAY DIFFRACTION94
2.4632-2.49840.29421400.286310217X-RAY DIFFRACTION98
2.4984-2.53560.29181410.275210245X-RAY DIFFRACTION99
2.5356-2.57510.31430.263210414X-RAY DIFFRACTION100
2.5751-2.61720.30421400.259510389X-RAY DIFFRACTION100
2.6172-2.66230.30021390.247710441X-RAY DIFFRACTION100
2.6623-2.71060.29031410.248310415X-RAY DIFFRACTION100
2.7106-2.76260.30811380.245310339X-RAY DIFFRACTION100
2.7626-2.81880.25171420.233510381X-RAY DIFFRACTION100
2.8188-2.87990.23361430.225810477X-RAY DIFFRACTION100
2.8799-2.94670.29871430.220110432X-RAY DIFFRACTION100
2.9467-3.02020.28281410.227610401X-RAY DIFFRACTION100
3.0202-3.10150.25961410.218810304X-RAY DIFFRACTION100
3.1015-3.19240.25881420.21210453X-RAY DIFFRACTION100
3.1924-3.29510.22151390.20910341X-RAY DIFFRACTION100
3.2951-3.41230.23081410.201110452X-RAY DIFFRACTION100
3.4123-3.54820.22581400.199410363X-RAY DIFFRACTION100
3.5482-3.70870.22491410.190610449X-RAY DIFFRACTION100
3.7087-3.90280.21081370.170210385X-RAY DIFFRACTION100
3.9028-4.14530.16911400.154810364X-RAY DIFFRACTION100
4.1453-4.46210.18751450.144510439X-RAY DIFFRACTION100
4.4621-4.90510.11971430.140110411X-RAY DIFFRACTION100
4.9051-5.60120.15071420.162310368X-RAY DIFFRACTION100
5.6012-7.00590.2051360.20610430X-RAY DIFFRACTION100
7.0059-19.97760.14811390.147710387X-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)
1-0.04130.1251-0.0102-0.0379-0.0372-0.03130.0395-0.22020.4331-0.04950.01030.41590.07570.202800.5168-0.0306-0.05570.50450.04650.394545.643956.0738253.0081
20.33020.439-0.4879-0.34890.34560.3078-0.16340.1129-0.09520.44180.1629-0.10460.1269-0.1464-00.22710.05170.08410.32820.05360.18680.778345.4532240.807
30.11530.0127-0.28240.19320.16660.2777-0.3575-0.14370.16520.09170.1312-0.038-0.1285-0.0757-00.32930.0809-0.04470.27140.01880.282517.677652.9928243.9399
40.0462-0.04920.03180.01620.04760.1144-0.1523-0.00360.38680.25020.06570.1832-0.305-0.163200.4160.1730.04850.4763-0.02290.4068-6.686251.7564244.0854
50.2101-0.14380.06490.0998-0.1430.2333-0.2371-0.0236-0.02490.01770.13280.0169-0.15150.0521-00.37820.0205-0.11950.2318-0.01280.296525.701461.1756236.3616
6-0.0071-0.005-0.04630.0044-0.0081-0.03680.0130.2424-0.22520.05010.4042-0.088-0.3414-0.2295-00.70560.0853-0.0250.48870.10340.255430.691554.8363214.6862
70.1078-0.09230.0233-0.04-0.01410.0248-0.31880.0016-0.21040.2020.32580.24540.01830.5409-00.11930.1086-0.10840.2885-0.11730.25745.200633.0612221.7771
80.0451-0.2661-0.5167-0.06150.05750.48880.04830.08750.09550.03270.0116-0.1032-0.1007-0.024800.29080.0027-0.03940.20340.01360.308727.080645.4627220.0639
9-0.0455-0.0233-0.07620.3939-0.16130.1830.02770.0143-0.03980.10140.0133-0.11590.0284-0.0313-00.28760.0187-0.09780.2579-0.010.28141.362938.1077240.052
100.02230.00570.01660.0253-0.00840.0121-0.5792-0.25520.03310.1358-0.4187-0.25010.27-0.0339-00.93840.0394-0.59191.0946-0.04510.978858.888934.4288261.2691
110.1726-0.00610.02380.2801-0.14130.32710.11350.16430.06690.1246-0.0993-0.0820.0005-0.024400.42950.0122-0.07670.30660.02540.369941.410941.706246.228
12-0.0876-0.2481-0.23480.39640.22420.1482-0.00040.0631-0.02050.0492-0.01-0.0297-0.0256-0.0593-00.2074-0.0206-0.01740.2445-0.020.241217.959933.6725208.2219
13-0.146-0.08950.05270.3340.34620.11070.02080.052-0.0540.0179-0.085-0.0529-0.08360.0078-00.2496-0.0348-0.00060.2821-0.02890.309819.989318.5458193.5673
14-0.03050.2144-0.03030.16460.36410.32350.0810.0081-0.00870.0284-0.1383-0.04260.1173-0.1457-00.24790.00790.00350.2478-0.05210.244415.46379.8279173.4137
150.14520.01720.19480.05280.2160.1180.0622-0.0005-0.0175-0.0233-0.1999-0.0049-0.0606-0.1049-00.3739-0.0255-0.00050.3337-0.04540.374917.601319.1466173.7394
160.2485-0.2142-0.12180.83530.16250.0795-0.0293-0.02190.0171-0.1035-0.240.1327-0.1196-0.3947-00.19380.0598-0.02310.3975-0.08530.25825.76951.0402142.4106
170.04280.0377-0.0997-0.0083-0.27180.0762-0.1098-0.0235-0.0107-0.08120.0346-0.09420.1323-0.0628-00.29190.03090.03230.3026-0.03650.330531.3509-2.1738168.0379
180.0554-0.0053-0.01390.2661-0.1386-0.0392-0.04930.00390.09930.0222-0.1602-0.1510.6557-0.175500.45250.13240.00980.25140.05880.379239.6947-11.6657178.2632
190.14810.1135-0.28910.37140.55330.46660.00530.0161-0.0207-0.0526-0.0733-0.0388-0.0578-0.157800.2710.04810.00780.3142-0.03190.296314.05340.5154138.2062
20-0.0012-0.02610.02760.0135-0.0050.0019-0.07450.0636-0.18480.10670.23740.1742-0.0754-0.11500.7263-0.21970.09160.6611-0.12890.457214.8608-32.1373129.4916
210.1015-0.1130.07390.06-0.01390.0459-0.01370.033-0.0590.03640.0282-0.09960.16360.140700.28780.06940.10320.3199-0.05250.377665.7965-22.2384114.7955
220.1638-0.22-0.1334-0.40540.54980.1194-0.199-0.07820.011-0.10790.18030.0980.27720.047900.26070.08840.11490.2951-0.05620.294459.2076-28.0335110.6435
230.12410.14630.00030.0872-0.110.0544-0.11340.4393-0.0251-0.0610.1649-0.0138-0.06220.3727-00.27570.07070.09260.4803-0.09710.345372.9806-23.7659110.0139
240.2618-0.2729-0.26750.21120.39110.39940.02720.07740.0302-0.0732-0.0219-0.0122-0.0643-0.103500.3194-0.00770.05830.29740.00530.264339.6673-16.0845106.0872
250.3014-0.0246-0.06820.11110.0309-0.0138-0.06290.13440.0962-0.0617-0.00040.0444-0.0703-0.23100.2673-0.02190.03410.26380.00020.31634.1961-7.9841113.3587
260.24390.2778-0.23760.54330.07910.5695-0.05230.00920.01220.04120.0006-0.0350.1112-0.068700.27170.00330.05150.2274-0.01960.252332.2205-28.7004120.097
270.0309-0.144-0.2545-0.0867-0.00820.40240.0049-0.08470.0135-0.08920.0198-0.0034-0.01140.115500.28790.01360.02920.2933-0.03620.330345.8007-6.9472136.5488
28-0.00010.0080.05180.0452-0.06780.04590.0364-0.0126-0.2011-0.43320.177-0.2036-0.5536-0.0195-00.40320.03130.0420.2809-0.02830.202827.709928.9381166.6542
29-0.3103-0.009-0.1007-0.14610.02850.55360.0077-0.02740.0032-0.04560.02920.0193-0.01620.050100.30240.0150.01970.3204-0.02890.30838.41093.0386154.8491
300.10380.06330.1260.2102-0.03510.46570.02260.0683-0.07930.0354-0.0110.1216-0.0830.232900.0758-0.02110.02530.158-0.03720.154548.106415.8494178.4307
310.1218-0.2235-0.08330.4188-0.01850.1545-0.0818-0.0245-0.0026-0.02990.0638-0.21050.09720.1719-00.17140.044-0.07230.3924-0.02350.334661.207518.0791202.555
320.15940.0063-0.01380.19530.0390.04340.025-0.09420.05770.191-0.0259-0.00170.09290.0167-00.3029-0.006-0.02570.21740.01020.242939.0573-0.3301191.1585
330.22740.0404-0.13810.0719-0.0240.20740.0215-0.05150.0614-0.00220.0131-0.02240.14310.145200.38770.0065-0.09290.46-0.00030.416157.278314.3773202.6841
340.3372-0.2678-0.0750.05430.45490.491-0.0576-0.0597-0.01330.09360.07340.0804-0.04390.160600.3002-0.0113-0.01240.3057-0.02730.31146.748822.6878206.5823
35-0.00120.01730.00780.0009-0.0073-0.001-0.0894-0.001-0.082-0.0679-0.08950.00270.0169-0.0468-01.52790.0108-0.41351.4006-0.02291.242532.400431.7312261.2885
36-0.00270.0103-0.00480.0044-0.0040.00690.1636-0.02690.19930.19680.0305-0.0738-0.0318-0.127300.904-0.0036-0.08550.6742-0.0970.535231.429820.8986260.9308
370.0169-0.02570.01120.0027-0.02940.0098-0.4185-0.09640.01250.0122-0.2065-0.4999-0.2209-0.353800.3916-0.1567-0.13290.7903-1.0314-0.418224.099913.2068242.6941
380.00230.03240.01090.0062-0.03070.0186-0.1826-0.20220.3764-0.20240.22820.2270.0469-0.392-00.5497-0.27980.05140.9703-0.25990.722918.46525.1838223.3337
390.0088-0.0028-0.01480.01650.00090.0078-0.1728-0.31160.2665-0.0102-0.16550.25360.0652-0.1376-00.6514-0.21320.03590.394-0.01640.405215.3301-5.5601209.2524
400.0187-0.00780.0024-0.0047-0.00480.0050.2597-0.2252-0.1322-0.17580.03660.01920.1328-0.1217-00.7609-0.20310.03770.4926-0.05330.376415.0091-15.6498192.0057
410.0009-0.00220.0019-0.00140.0031-0.0151-0.07650.0413-0.0006-0.0641-0.10330.0889-0.0676-0.1547-01.27430.0215-0.06010.94550.11371.51073.3409-5.6222181.1846
420.01270.0061-0.01020.0169-0.0070.00320.2151-0.1089-0.15630.0003-0.02430.2773-0.1574-0.072-00.4879-0.04780.04840.5219-0.06670.39167.38786.4336194.7578
43-0.00670.00570.0115-0.0050.00740.00810.01940.20020.0028-0.03620.08230.21620.0037-0.1862-00.4719-0.0158-0.05610.658-0.16730.48819.119218.9565208.6816
440.01020.00460.01120.01520.03210.0167-0.43240.1336-0.43330.26730.1198-0.06610.15010.0042-00.5952-0.0310.06190.3680.0630.38329.203720.5981225.5763
450.0058-0.0025-0.01130.005-0.00370.0117-0.1221-0.11970.1610.0426-0.02360.19-0.014-0.0109-00.6883-0.0080.16750.5775-0.04570.48483.12129.4456233.9794
460.00490.0185-0.00070.00630.00330.001-0.22010.0915-0.1322-0.1153-0.12950.01980.0327-0.0949-00.4483-0.14540.12740.7142-0.02230.6185-14.156234.8568226.4794
470.0258-0.0459-0.0041-0.0277-0.02170.00830.0570.135-0.1401-0.0371-0.15140.23910.0643-0.185800.40130.042-0.03310.5734-0.0310.4607-1.656634.7185216.644
480.00190.008-0.00330.0083-0.0030.00760.08730.04530.06880.0692-0.01590.1351-0.11160.0854-00.70660.30760.04351.06330.16230.47491.633637.9569200.3934
490.0046-0.00040.00030.0021-0.0047-0.0008-0.0078-0.00820.02720.06230.01220.03610.00990.066301.29010.1840.03491.65340.07641.25741.631741.2314190.2299
500.1069-0.06310.1259-0.01930.0655-0.0843-0.374-0.0710.3552-0.15720.0327-0.01590.4651-0.269700.86720.2069-0.1810.7807-0.18960.7961-0.50997.434168.7486
510.0017-0.0034-0.00460.0002-0.00470.00130.057-0.06250.0999-0.00970.02680.1706-0.0126-0.074601.0089-0.06820.09361.34030.05970.8483-1.62795.5375174.7661
520-0.00060.00090.0062-0.00480.00130.0412-0.0213-0.13560.09340.0404-0.05470.0297-0.024-0.00011.5823-0.3110.03051.89230.27361.4302-2.398312.8891183.3288
530.00640.0027-0.00430.00210.00430.00060.015-0.01250.0113-0.02110.038-0.04440.01810.006400.38340.05330.03190.60510.00450.56211.674224.5053203.2764
54-0.011-0.0045-0.00230.00270.00840.00610.1542-0.02720.3071-0.072-0.19840.06890.1474-0.2351-00.39120.1969-0.03410.60220.01480.4636.826631.0013194.3738
550.0082-0.0024-0.0007-0.00110.0025-0.0005-0.0052-0.05790.05640.07640.0304-0.0730.01580.0401-00.83270.1737-0.34830.6603-0.09020.608443.454626.7947263.3893
560.0198-0.0129-0.00010.02420.0336-0.0099-0.00010.1024-0.08510.3406-0.083-0.0901-0.0166-0.1095-00.465-0.0218-0.03960.3679-0.04740.425338.040620.6485248.8674
57-0.01720.0258-0.0264-0.0011-0.02760.0281-0.3622-0.1574-0.0622-0.1327-0.22360.2525-0.1368-0.0923-00.61250.0896-0.1280.4027-0.0630.46929.005212.9773226.172
58-0.0004-0.00040.0128-0.00510.00890.004-0.3234-0.14630.0074-0.069-0.01430.13870.0064-0.067800.3403-0.0811-0.03990.3371-0.02080.324621.01524.7932207.8812
590.0012-0.0030.00180.0293-0.0067-0.0186-0.2319-0.1847-0.2704-0.2683-0.3072-0.0205-0.1627-0.3336-00.464-0.09690.02270.3506-0.08250.432511.8047-2.7767194.2186
600.00230.00090.00070.01110.00010.00090.1856-0.0219-0.1305-0.0899-0.0599-0.08150.068-0.084101.1596-0.4051-0.41380.1167-0.18120.280224.2549-10.3776219.9587
610.00130.01150.0011-0.00230.0010.00480.2495-0.0113-0.0780.03760.10130.1630.1163-0.1687-00.9508-0.6849-0.2910.6535-0.3482-0.059822.2699-6.6236227.1601
62-0.00090.03130.0022-0.00670.01660.0032-0.571-0.14730.0060.1550.02720.00320.0548-0.249-00.2593-2.0974-0.54470.4841-1.3251-0.158920.25332.9293239.6128
630.045-0.0514-0.0329-0.00310.00380.0295-0.11810.3038-0.18030.3143-0.33350.0773-0.0244-0.156500.7659-0.18090.12441.1778-0.1210.380125.853410.9082260.1938
640.0072-0.0114-0.0063-0.0031-0.00390.0061-0.1125-0.0625-0.08590.1420.1418-0.04450.22430.038900.611-0.1045-0.04250.6577-0.06150.539933.9759.6743257.3505
650.0404-0.07210.0050.00620.02270.00450.07020.01490.16650.2592-0.27320.15030.2922-0.177900.6336-0.15710.01380.38-0.01640.237730.93844.1086236.4917
660.02430.0061-0.0010.00610.01720.01250.00160.06630.17680.1774-0.2151-0.00370.26840.1645-00.5777-0.05620.06040.286-0.00450.333726.9951-3.0247213.4456
670.0084-0.021-0.01350.0049-0.0530.0373-0.08520.12490.00810.015-0.1102-0.1170.08460.1366-00.4205-0.0763-0.00790.33820.01540.382922.4493-7.9669190.6185
680.01420.02120.02330.01370.00170.0124-0.0474-0.1328-0.34740.0352-0.0539-0.0230.3255-0.2072-00.5141-0.00190.03720.2806-0.03230.322120.1928-12.0716169.1486
690.01210.04750.03710.05020.05110.0255-0.03310.17870.05560.0448-0.47290.2530.30540.1637-00.64750.16030.06510.5236-0.05670.396445.7899-18.3926152.1991
70-0.00180.00640.0053-0.00640.02040.0018-0.1107-0.2667-0.37470.19260.1475-0.2835-0.0913-0.031500.59590.18960.07230.4710.00730.65862.3924-31.4955130.1721
710.07350.11110.09870.0196-0.0039-0.04840.24851.5571-1.2692-0.47910.0075-0.20840.87531.4362-0-0.98821.53380.9814-0.4598-0.8732-0.338550.0041-44.5415116.4606
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 5:68)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 69:144)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 145:185)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 186:223)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 224:334)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 335:350)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 351:382)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 383:439)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 440:521)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 522:546)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 547:617)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 618:738)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 739:806)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 807:873)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 874:920)
16X-RAY DIFFRACTION16(CHAIN A AND RESID 921:998)
17X-RAY DIFFRACTION17(CHAIN A AND RESID 999:1036)
18X-RAY DIFFRACTION18(CHAIN A AND RESID 1037:1098)
19X-RAY DIFFRACTION19(CHAIN A AND RESID 1099:1227)
20X-RAY DIFFRACTION20(CHAIN A AND RESID 1237:1250)
21X-RAY DIFFRACTION21(CHAIN B AND RESID 7:66)
22X-RAY DIFFRACTION22(CHAIN B AND RESID 67:143)
23X-RAY DIFFRACTION23(CHAIN B AND RESID 144:186)
24X-RAY DIFFRACTION24(CHAIN B AND RESID 187:314)
25X-RAY DIFFRACTION25(CHAIN B AND RESID 315:368)
26X-RAY DIFFRACTION26(CHAIN B AND RESID 369:534)
27X-RAY DIFFRACTION27(CHAIN B AND RESID 535:624)
28X-RAY DIFFRACTION28(CHAIN B AND RESID 625:660)
29X-RAY DIFFRACTION29(CHAIN B AND RESID 661:768)
30X-RAY DIFFRACTION30(CHAIN B AND RESID 769:850)
31X-RAY DIFFRACTION31(CHAIN B AND RESID 851:917)
32X-RAY DIFFRACTION32(CHAIN B AND RESID 918:968)
33X-RAY DIFFRACTION33(CHAIN B AND RESID 969:1017)
34X-RAY DIFFRACTION34(CHAIN B AND RESID 1018:1121)
35X-RAY DIFFRACTION35(CHAIN D AND RESID 15:22)
36X-RAY DIFFRACTION36(CHAIN D AND RESID 23:33)
37X-RAY DIFFRACTION37(CHAIN D AND RESID 34:49)
38X-RAY DIFFRACTION38(CHAIN D AND RESID 50:62)
39X-RAY DIFFRACTION39(CHAIN D AND RESID 63:73)
40X-RAY DIFFRACTION40(CHAIN D AND RESID 74:87)
41X-RAY DIFFRACTION41(CHAIN D AND RESID 88:98)
42X-RAY DIFFRACTION42(CHAIN D AND RESID 99:106)
43X-RAY DIFFRACTION43(CHAIN D AND RESID 107:111)
44X-RAY DIFFRACTION44(CHAIN D AND RESID 112:125)
45X-RAY DIFFRACTION45(CHAIN D AND RESID 126:132)
46X-RAY DIFFRACTION46(CHAIN D AND RESID 133:144)
47X-RAY DIFFRACTION47(CHAIN D AND RESID 145:162)
48X-RAY DIFFRACTION48(CHAIN D AND RESID 163:169)
49X-RAY DIFFRACTION49(CHAIN D AND RESID 170:176)
50X-RAY DIFFRACTION50(CHAIN D AND RESID 177:501)
51X-RAY DIFFRACTION51(CHAIN D AND RESID 502:511)
52X-RAY DIFFRACTION52(CHAIN D AND RESID 512:516)
53X-RAY DIFFRACTION53(CHAIN D AND RESID 527:532)
54X-RAY DIFFRACTION54(CHAIN D AND RESID 533:543)
55X-RAY DIFFRACTION55(CHAIN E AND RESID 6:13)
56X-RAY DIFFRACTION56(CHAIN E AND RESID 14:29)
57X-RAY DIFFRACTION57(CHAIN E AND RESID 30:46)
58X-RAY DIFFRACTION58(CHAIN E AND RESID 47:58)
59X-RAY DIFFRACTION59(CHAIN E AND RESID 59:72)
60X-RAY DIFFRACTION60(CHAIN F AND RESID 0:5)
61X-RAY DIFFRACTION61(CHAIN F AND RESID 6:12)
62X-RAY DIFFRACTION62(CHAIN F AND RESID 13:26)
63X-RAY DIFFRACTION63(CHAIN F AND RESID 27:44)
64X-RAY DIFFRACTION64(CHAIN F AND RESID 45:53)
65X-RAY DIFFRACTION65(CHAIN F AND RESID 54:73)
66X-RAY DIFFRACTION66(CHAIN F AND RESID 74:86)
67X-RAY DIFFRACTION67(CHAIN F AND RESID 87:104)
68X-RAY DIFFRACTION68(CHAIN F AND RESID 105:116)
69X-RAY DIFFRACTION69(CHAIN F AND RESID 117:130)
70X-RAY DIFFRACTION70(CHAIN F AND RESID 131:139)
71X-RAY DIFFRACTION71(CHAIN F AND RESID 140:155)

+
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