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- PDB-5buz: Crystal Structure of a Complex Between the SNARE Vam3 and the HOP... -

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Basic information

Entry
Database: PDB / ID: 5buz
TitleCrystal Structure of a Complex Between the SNARE Vam3 and the HOPS Vps33-Vps16 subcomplex from Chaetomium thermophilum
Components
  • Putative vacuolar protein sorting-associated protein
  • SM (Sec1/Munc18-like) protein
  • SNAP receptor-like protein
KeywordsTRANSPORT PROTEIN / Membrane trafficking / SM protein / HOPS complex / thermophile / SNARE domain
Function / homology
Function and homology information


HOPS complex / vacuole fusion, non-autophagic / Golgi to vacuole transport / vesicle docking / SNAP receptor activity / SNARE complex / vesicle fusion / endosomal transport / ligase activity / vesicle-mediated transport ...HOPS complex / vacuole fusion, non-autophagic / Golgi to vacuole transport / vesicle docking / SNAP receptor activity / SNARE complex / vesicle fusion / endosomal transport / ligase activity / vesicle-mediated transport / endomembrane system / SNARE binding / intracellular protein transport / actin binding / endosome
Similarity search - Function
Syntaxin-like protein / Sec1/Munc18 (SM) protein, domain 3b / Vps16, C-terminal / Vps16, N-terminal / Vacuolar protein sorting-associated protein 16 / Vps16, C-terminal domain superfamily / Vps16, C-terminal region / Vps16, N-terminal region / Vacuolar protein sorting-associated protein 33, domain 3b / Sec1/Munc18 (SM) protein, domain 2 ...Syntaxin-like protein / Sec1/Munc18 (SM) protein, domain 3b / Vps16, C-terminal / Vps16, N-terminal / Vacuolar protein sorting-associated protein 16 / Vps16, C-terminal domain superfamily / Vps16, C-terminal region / Vps16, N-terminal region / Vacuolar protein sorting-associated protein 33, domain 3b / Sec1/Munc18 (SM) protein, domain 2 / Syntaxin Binding Protein 1; Chain A, domain 2 / Sec1/Munc18 (SM) protein, domain 3a / Sec1/Munc18 (SM) protein, domain 1 / Sec1-like, domain 1 / Sec1-like protein / Sec1-like, domain 2 / Sec1-like superfamily / Sec1-like, domain 3a / Sec1 family / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / SNARE domain / Syntaxin / Syntaxin/epimorphin, conserved site / Syntaxin / epimorphin family signature. / SNARE / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / WD40/YVTN repeat-like-containing domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
SNAP receptor-like protein / Probable vacuolar protein sorting-associated protein 16 homolog / Small conjugating protein ligase-like protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsBaker, R.W. / Jeffrey, P.D. / Hughson, F.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071574 United States
Citation
Journal: Science / Year: 2015
Title: A direct role for the Sec1/Munc18-family protein Vps33 as a template for SNARE assembly.
Authors: Baker, R.W. / Jeffrey, P.D. / Zick, M. / Phillips, B.P. / Wickner, W.T. / Hughson, F.M.
#1: Journal: Plos One / Year: 2013
Title: Crystal Structures of the Sec1/Munc18 (SM) Protein Vps33, Alone and Bound to the Homotypic Fusion and Vacuolar Protein Sorting (HOPS) Subunit Vps16*
Authors: Baker, R.W. / Jeffrey, P.D. / Hughson, F.M.
History
DepositionJun 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SM (Sec1/Munc18-like) protein
B: Putative vacuolar protein sorting-associated protein
C: SNAP receptor-like protein
D: SM (Sec1/Munc18-like) protein
E: Putative vacuolar protein sorting-associated protein
F: SNAP receptor-like protein


Theoretical massNumber of molelcules
Total (without water)238,8136
Polymers238,8136
Non-polymers00
Water00
1
A: SM (Sec1/Munc18-like) protein
B: Putative vacuolar protein sorting-associated protein
C: SNAP receptor-like protein


Theoretical massNumber of molelcules
Total (without water)119,4073
Polymers119,4073
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-31 kcal/mol
Surface area45100 Å2
MethodPISA
2
D: SM (Sec1/Munc18-like) protein
E: Putative vacuolar protein sorting-associated protein
F: SNAP receptor-like protein


Theoretical massNumber of molelcules
Total (without water)119,4073
Polymers119,4073
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-35 kcal/mol
Surface area45190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.039, 95.950, 164.060
Angle α, β, γ (deg.)90.000, 99.120, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain D
12chain B
22chain E
13chain C
23chain F

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALALYSLYSchain AAA5 - 6587 - 660
21ALAALALYSLYSchain DDD5 - 6587 - 660
12SERSERGLYGLYchain BBB505 - 8284 - 327
22SERSERGLYGLYchain EEE505 - 8284 - 327
13GLUGLUGLUGLUchain CCC188 - 22510 - 47
23GLUGLUGLUGLUchain FFF186 - 2258 - 47

NCS ensembles :
ID
1
2
3

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Components

#1: Protein SM (Sec1/Munc18-like) protein / VPS33


Mass: 73990.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0057760 / Plasmid: pQLinkH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G0SCM5
#2: Protein Putative vacuolar protein sorting-associated protein / Vps16


Mass: 37912.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0026760 / Plasmid: pQLinkH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G0S6M7
#3: Protein SNAP receptor-like protein / VAM3


Mass: 7504.194 Da / Num. of mol.: 2 / Fragment: SNARE domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0015850 / Plasmid: pQLinkH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G0S236
Sequence detailsAuthors have indicated that the sequences in UniProt entries G0SCM5_CHATD and G0S236_CHATD are not correct

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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: 3.09 Å3/Da / Density % sol: 60.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: HEPES buffer, 8-10% w/v PEG 5000 monomethyl ether

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 2, 2014
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 54752 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 89.86 Å2 / Rmerge(I) obs: 0.102 / Χ2: 1.304 / Net I/av σ(I): 14.012 / Net I/σ(I): 6.3 / Num. measured all: 199852
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.1-3.153.60.86126870.49499.9
3.15-3.213.60.75927220.51499.9
3.21-3.273.70.66427250.512100
3.27-3.343.70.52127720.53899.9
3.34-3.413.70.40726790.57100
3.41-3.493.70.35327150.62299.9
3.49-3.583.70.29327480.712100
3.58-3.683.70.22426960.792100
3.68-3.783.70.19427130.896100
3.78-3.913.70.16627581.093100
3.91-4.043.70.14627231.222100
4.04-4.213.70.13127361.521100
4.21-4.43.70.11627421.821100
4.4-4.633.60.10927202.087100
4.63-4.923.60.09927392.19699.9
4.92-5.33.60.09727462.059100
5.3-5.833.60.09127401.749100
5.83-6.673.50.08127571.779100
6.67-8.43.70.06127792.258100
8.4-503.50.04128552.68699.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
CBASSdata collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KMO

4kmo


Resolution: 3.1→47.975 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2639 4.97 %Random selection
Rwork0.1935 50487 --
obs0.1955 53126 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 300.87 Å2 / Biso mean: 104.7949 Å2 / Biso min: 35.85 Å2
Refinement stepCycle: final / Resolution: 3.1→47.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15276 0 0 0 15276
Num. residues----1936
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315512
X-RAY DIFFRACTIONf_angle_d0.79720932
X-RAY DIFFRACTIONf_chiral_restr0.0292376
X-RAY DIFFRACTIONf_plane_restr0.0032734
X-RAY DIFFRACTIONf_dihedral_angle_d15.1125848
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5769X-RAY DIFFRACTION7.271TORSIONAL
12D5769X-RAY DIFFRACTION7.271TORSIONAL
21B3063X-RAY DIFFRACTION7.271TORSIONAL
22E3063X-RAY DIFFRACTION7.271TORSIONAL
31C287X-RAY DIFFRACTION7.271TORSIONAL
32F287X-RAY DIFFRACTION7.271TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.15640.33171250.329226702795100
3.1564-3.21710.32511520.298126162768100
3.2171-3.28270.30331290.260526542783100
3.2827-3.35410.28691270.243826002727100
3.3541-3.43210.25071390.235526612800100
3.4321-3.51790.2561410.229826682809100
3.5179-3.6130.27221410.220726112752100
3.613-3.71930.27751280.2226822810100
3.7193-3.83930.26571290.201826532782100
3.8393-3.97640.26621200.201326672787100
3.9764-4.13550.21941530.185826372790100
4.1355-4.32360.19521350.17526512786100
4.3236-4.55140.22651660.174826392805100
4.5514-4.83630.20171400.161226332773100
4.8363-5.20930.22921320.177326782810100
5.2093-5.73280.2951410.195426652806100
5.7328-6.56060.24751370.210926772814100
6.5606-8.25880.22731440.186427002844100
8.2588-47.98070.17771600.15512725288599
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)
10.6204-0.12440.18871.73960.00811.3230.121-0.24020.05950.3156-0.140.1415-0.09090.012800.4696-0.04930.11050.5262-0.11250.4553.59164.9411180.7418
20.4497-0.5719-0.1790.0415-0.39640.39830.0090.036-0.07060.0447-0.00210.13770.173-0.223200.3766-0.0336-0.03450.6251-0.12960.7058-18.37-8.8023167.604
30.5128-0.6092-0.37391.1166-0.58941.2227-0.14470.234-0.0307-0.3810.0101-0.08710.10410.4517-0.00530.61440.0279-0.05750.7011-0.00160.39576.3444-7.7363144.4691
40.0828-0.2735-0.23580.86590.27590.462-0.03440.24020.1524-0.1467-0.01740.24130.2863-0.0695-00.5960.0195-0.00810.5271-0.110.57441.3591-26.5193160.2492
50.65330.1896-0.01910.9622-0.16680.82030.15740.2292-0.0294-0.1248-0.21910.22410.31740.108400.4161-0.01050.03270.5076-0.0160.50781.9224-14.436167.5278
60.32820.02450.01490.26870.33190.2746-0.4176-0.7883-0.1230.5614-0.3214-0.607-0.33550.7039-0.10280.5472-0.0558-0.00381.24740.34841.015138.6914-2.6114182.1717
70.4112-0.0774-0.20470.311-0.30380.5080.02070.08360.12640.0333-0.18090.18020.0740.04670.00020.6088-0.09690.00550.70610.00760.734625.23055.5844170.928
80.18040.14760.05060.07270.30120.5949-0.10340.00830.1763-0.1279-0.0468-0.3392-0.19040.6710.00010.8993-0.0382-0.07960.79230.07180.730623.523110.7524148.8538
90.8291-0.0292-0.05910.84720.17861.3449-0.6940.8640.5592-1.46920.6111-0.0254-0.0529-0.30420.50471.1984-0.3989-0.46811.1130.30220.4077-3.74494.1921127.8434
100.04840.02990.0055-0.00050.004-0.0269-0.38430.4457-0.5817-0.12980.33620.14720.008-0.0278-0.00021.5415-0.5726-0.42541.84150.07792.015-33.7266-14.9287120.4184
110.0337-0.0154-0.0736-0.00840.0231-0.01080.410.04330.12831.05220.0538-0.87440.2773-0.317901.0989-0.05980.05961.8528-0.011.0793-43.2933-0.1077187.3579
120.06760.04190.0910.1086-0.03020.275-0.16380.6557-0.30410.0927-0.61740.1626-0.2159-0.1597-0.00730.72750.2649-0.15591.1551-0.35171.5158-17.01959.9216174.4028
130.6349-0.1879-0.0991.436-0.33541.57730.011-0.13950.04350.37980.0071-0.03640.2725-0.0301-00.68880.0946-0.04690.50690.05990.48523.35743.2362101.1616
140.1308-0.5850.9729-0.00410.4663-0.2025-0.02680.41510.11010.14750.0521-0.145-0.14190.22320.00390.44350.03690.0010.62380.05720.721726.196614.983287.4833
150.538-0.28220.16021.6950.75711.8429-0.00730.09770.0183-0.27580.0044-0.1433-0.28230.083600.50990.05370.03770.36840.05470.54244.715421.148474.946
160.3209-0.52110.47290.8839-0.77860.74010.4033-0.7951-0.0330.19860.35560.99570.84230.39180.18170.45480.02050.13460.9997-0.32150.724-30.58788.7222102.844
170.216-0.0527-0.01130.19320.37350.8396-0.15320.1612-0.1814-0.3118-0.1151-0.24020.3577-0.517-0.00110.6924-0.0318-0.02620.448-0.03260.7875-17.26771.357891.3835
180.2414-0.0199-0.15450.0527-0.09860.3851-0.01280.2322-0.14850.402-0.01790.6540.3243-0.43520.00010.81790.0213-0.05090.47910.03830.7632-15.4276-5.24570.0752
190.24240.07250.11070.3071-0.38040.6752-0.20410.6514-0.2092-0.50440.1974-0.06480.55230.22570.00530.7770.19230.18590.7303-0.10420.63389.4704-4.211149.8001
200.05840.11560.04010.05820.14380.0543-0.36440.20630.30560.4337-0.1461-0.22430.8490.4878-0.00460.6585-0.09080.09861.62950.06441.088837.799614.441.8255
210.05020.11580.09190.0033-0.04870.05140.08460.2875-0.44520.06540.030.4251-0.19010.38980.00020.90220.1529-0.14781.49110.03481.224651.27127.0393109.8948
220.3056-0.0334-0.46870.1850.21750.8939-0.45990.02760.07150.628-0.4086-0.53630.3339-0.3483-0.04850.79790.1324-0.14621.16610.21511.203923.7584-3.117395.5413
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 215 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 216 through 379 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 380 through 479 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 480 through 565 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 566 through 658 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 505 through 544 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 545 through 605 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 606 through 657 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 658 through 790 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 791 through 828 )B0
11X-RAY DIFFRACTION11chain 'C' and (resid 188 through 212 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 213 through 225 )C0
13X-RAY DIFFRACTION13chain 'D' and (resid 5 through 215 )D0
14X-RAY DIFFRACTION14chain 'D' and (resid 216 through 379 )D0
15X-RAY DIFFRACTION15chain 'D' and (resid 380 through 658 )D0
16X-RAY DIFFRACTION16chain 'E' and (resid 505 through 546 )E0
17X-RAY DIFFRACTION17chain 'E' and (resid 547 through 605 )E0
18X-RAY DIFFRACTION18chain 'E' and (resid 606 through 657 )E0
19X-RAY DIFFRACTION19chain 'E' and (resid 658 through 769 )E0
20X-RAY DIFFRACTION20chain 'E' and (resid 770 through 828 )E0
21X-RAY DIFFRACTION21chain 'F' and (resid 186 through 212 )F0
22X-RAY DIFFRACTION22chain 'F' and (resid 213 through 225 )F0

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Yorodumi

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  • 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

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