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- PDB-4n63: Crystal structure of hemagglutinin from an H7N9 influenza virus i... -

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Basic information

Entry
Database: PDB / ID: 4n63
TitleCrystal structure of hemagglutinin from an H7N9 influenza virus in complex with an O-linked glycan receptor
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN / viral envelope protein / hemagglutinin / viral fusion protein
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / metal ion binding
Similarity search - Function
Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Ribbon / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7522 Å
AuthorsXu, R. / Wilson, I.A.
CitationJournal: Science / Year: 2013
Title: Preferential recognition of avian-like receptors in human influenza A H7N9 viruses.
Authors: Xu, R. / de Vries, R.P. / Zhu, X. / Nycholat, C.M. / McBride, R. / Yu, W. / Paulson, J.C. / Wilson, I.A.
History
DepositionOct 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin HA1
B: Hemagglutinin HA2
C: Hemagglutinin HA1
D: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,5518
Polymers112,1504
Non-polymers2,4014
Water1,11762
1
A: Hemagglutinin HA1
B: Hemagglutinin HA2
hetero molecules

A: Hemagglutinin HA1
B: Hemagglutinin HA2
hetero molecules

A: Hemagglutinin HA1
B: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,79515
Polymers168,2246
Non-polymers4,5709
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544-z,x-1/2,-y-1/21
crystal symmetry operation11_545y+1/2,-z-1/2,-x1
Buried area37900 Å2
ΔGint-79 kcal/mol
Surface area57890 Å2
MethodPISA
2
C: Hemagglutinin HA1
D: Hemagglutinin HA2
hetero molecules

C: Hemagglutinin HA1
D: Hemagglutinin HA2
hetero molecules

C: Hemagglutinin HA1
D: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,8589
Polymers168,2246
Non-polymers2,6333
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area35080 Å2
ΔGint-108 kcal/mol
Surface area57560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.608, 153.608, 153.608
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11B-309-

HOH

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Components

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Hemagglutinin ... , 2 types, 4 molecules ACBD

#1: Protein Hemagglutinin HA1


Mass: 34993.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Shanghai/2/2013 / Gene: HA, hemagglutinin / Plasmid: pFastbac-HT / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: R4NN21
#2: Protein Hemagglutinin HA2


Mass: 21081.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Shanghai/2/2013 / Gene: HA, hemagglutinin / Plasmid: pFastbac-HT / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: R4NN21

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Sugars , 3 types, 4 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose


Type: oligosaccharide / Mass: 877.796 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpNAcb1-3DGalpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[a2112h-1b_1-5_2*NCC/3=O][a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3-4/a3-b1_b4-c1_c3-d2WURCSPDB2Glycan 1.1.0
[][b-D-GalpNAc]{[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 1 types, 62 molecules

#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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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: 2.69 Å3/Da / Density % sol: 54.33 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 17-20% PEG3350, 0.2 M ammonium acetate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295.5K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0331 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 16, 2013 / Details: K-B pair of biomorph mirrors
RadiationMonochromator: double crystal monochromator and K-B pair of biomorph mirrors for vertical and horizontal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0331 Å / Relative weight: 1
ReflectionRedundancy: 4.4 % / Number: 137382 / Rmerge(I) obs: 0.095 / Χ2: 1.02 / D res high: 2.75 Å / D res low: 50 Å / Num. obs: 31335 / % possible obs: 99.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.925093.910.0491.0454.4
4.75.9298.510.0741.0064.4
4.114.799.410.0691.0344.4
3.734.1110010.0850.9894.4
3.463.7310010.121.014.4
3.263.4610010.1681.0974.4
3.13.2610010.2521.0884.4
2.963.110010.3921.0224.4
2.852.9610010.5520.974.4
2.752.8510010.7940.9734.4
ReflectionResolution: 2.75→50 Å / Num. obs: 31335 / % possible obs: 99.1 % / Rmerge(I) obs: 0.095

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 37.66 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.75 Å42.6 Å
Translation2.75 Å42.6 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4N5J

4n5j


Resolution: 2.7522→42.603 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.4 / σ(F): 1.34 / Phase error: 28.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2693 1584 5.06 %
Rwork0.2133 --
obs0.2161 31323 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 97.8468 Å2
Refinement stepCycle: LAST / Resolution: 2.7522→42.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7600 0 162 62 7824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037923
X-RAY DIFFRACTIONf_angle_d0.75710702
X-RAY DIFFRACTIONf_dihedral_angle_d17.8612959
X-RAY DIFFRACTIONf_chiral_restr0.0341181
X-RAY DIFFRACTIONf_plane_restr0.0031401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7522-2.8410.36581360.29432716X-RAY DIFFRACTION100
2.841-2.94260.35431510.28072684X-RAY DIFFRACTION100
2.9426-3.06030.3191360.27342716X-RAY DIFFRACTION100
3.0603-3.19960.3481480.272712X-RAY DIFFRACTION100
3.1996-3.36820.31581350.24972689X-RAY DIFFRACTION100
3.3682-3.57910.26811580.23482695X-RAY DIFFRACTION100
3.5791-3.85530.29141450.21992703X-RAY DIFFRACTION100
3.8553-4.2430.25961590.19512698X-RAY DIFFRACTION100
4.243-4.85620.21511440.1752724X-RAY DIFFRACTION99
4.8562-6.11540.2241460.19142702X-RAY DIFFRACTION98
6.1154-42.60830.26321260.19352700X-RAY DIFFRACTION94
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)
14.51912.6699-4.51922.3199-3.17665.38950.5972-1.07440.41980.6452-0.56880.4168-0.44190.8225-0.03450.5856-0.23020.06910.701-0.12780.424927.6799-41.0073-7.3006
23.79720.3746-1.55834.7531-2.8864.0130.4765-0.1512-0.180.0862-0.30760.8727-0.2160.4523-0.17920.47240.06750.07150.4368-0.1410.5245-10.315-65.889414.3394
36.84740.1364-4.93652.04920.49429.78560.9485-0.90430.66290.6356-0.39620.2971-0.80490.0247-0.42330.6831-0.23350.13170.6684-0.06410.376115.2556-46.90410.4773
46.37134.9959-5.15896.8009-5.01237.18120.4175-1.3471-0.27990.6678-0.925-0.8782-0.3850.89610.45020.4455-0.0634-0.09630.5971-0.04210.382837.3974-41.6686-14.2424
52.0236.57263.56562.02833.11936.2215-0.3086-0.047-1.44041.95080.5805-2.9785-0.6581.43190.01170.7199-0.1993-0.07340.6660.02460.658551.148-29.4806-27.6541
66.25294.2224-2.71227.8893-5.25756.01610.0188-0.25660.82560.9835-0.0903-0.2406-0.74790.23240.07380.5165-0.1611-0.01340.4795-0.14390.527344.6639-21.8559-23.9055
72.19757.1798-8.12452.1135-7.81212.23340.10911.42190.80320.541.0621.5132-0.2011-1.075-0.97260.6566-0.08610.16060.7090.06710.756425.853-32.5986-22.0465
82.10167.2694-7.64355.1221-4.58166.1468-0.2341.5982.802-0.63951.5931.1129-0.4044-0.3719-1.56310.7876-0.20190.14490.87630.31721.26128.6745-50.2287-8.1234
95.1004-0.61611.13852.01262.00912.0190.3749-0.9210.13590.92820.4272-0.25270.43530.4725-0.46550.8060.03180.04670.8737-0.04920.513110.0689-64.75056.5631
106.11065.8085-6.1823.3553-5.35356.6681-0.28120.0127-0.3042-0.38640.0709-0.28810.32250.02180.15050.4742-0.07540.05770.3881-0.01160.365227.8204-47.812-20.4474
113.8771-2.50940.67385.5069-0.90867.6448-0.23110.20080.7157-0.85560.1741-0.7852-0.50760.45340.04410.4944-0.15640.08250.34680.01730.640347.6937-17.47-40.7543
121.5542-1.2325-1.30721.88340.83640.7927-0.14010.076-0.3904-0.41930.235-0.2456-0.0057-0.0330.06581.42250.22740.6291.8556-0.60171.34758.8308-45.61441.7994
133.70430.73330.79854.38462.08562.99250.62030.1233-0.0464-0.4554-0.4335-0.15870.4563-0.3812-0.19710.91870.0918-0.01690.8034-0.26920.66621.4339-26.529829.728
141.05970.3452-0.80032.99161.27241.44960.09710.58540.1537-0.3903-0.43730.0974-0.20050.61360.01631.48330.42960.47321.528-0.44761.195846.1311-39.12758.6676
153.4791-3.2094-2.73115.26323.16273.4154-0.02380.02330.5682-0.1751-0.0727-0.5784-0.51170.9052-0.4311.07560.17990.7761.5208-0.5451.875769.7679-50.39671.6796
165.38860.5443-5.52753.91090.40812.0021-0.5912-1.59732.01170.290.00660.1913-2.01012.05650.58381.75890.18030.29422.0943-0.37871.336583.9559-63.6701-10.4372
170.1860.55420.72723.09972.02982.8283-0.3009-0.28910.1924-0.16410.65160.5808-0.40250.6277-0.25861.25770.22430.51411.8054-0.57121.789675.9733-62.3828-17.372
187.268-3.9013-3.78587.07192.29735.8759-0.2622-0.2156-0.09990.090.01410.3511-0.2992-0.55760.03321.36770.05050.53892.0585-0.77691.546358.784-61.5506-4.0025
192.8636-2.6721-2.83782.49672.63662.6842-0.57450.6797-1.2781-0.4802-0.00120.18870.3729-0.39710.58761.4113-0.05260.37481.9153-0.48581.255142.0359-47.669814.1129
204.8726-0.74924.30655.0568-3.92035.94670.1077-0.03530.3244-0.30620.0625-0.2155-1.0175-0.1254-0.12881.21730.41470.32341.4868-0.39091.250242.8183-30.658725.8975
211.6235-1.6469-1.62792.02262.69522.7694-0.20720.2738-0.5012-0.29990.1954-0.47390.1980.44950.06431.49070.30320.71521.4658-0.57961.670262.6014-57.090610.2879
220.7350.3032-0.00171.7468-0.05133.4492-0.2890.4248-0.335-0.0443-0.09690.06560.8530.3780.22441.12460.42751.38742.2247-1.72131.842281.2584-79.0507-19.7121
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 65 )
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 269 )
3X-RAY DIFFRACTION3chain 'A' and (resid 270 through 308 )
4X-RAY DIFFRACTION4chain 'A' and (resid 309 through 327 )
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 11 )
6X-RAY DIFFRACTION6chain 'B' and (resid 12 through 37 )
7X-RAY DIFFRACTION7chain 'B' and (resid 38 through 56 )
8X-RAY DIFFRACTION8chain 'B' and (resid 57 through 66 )
9X-RAY DIFFRACTION9chain 'B' and (resid 67 through 74 )
10X-RAY DIFFRACTION10chain 'B' and (resid 75 through 126 )
11X-RAY DIFFRACTION11chain 'B' and (resid 127 through 172 )
12X-RAY DIFFRACTION12chain 'C' and (resid 11 through 65 )
13X-RAY DIFFRACTION13chain 'C' and (resid 66 through 269 )
14X-RAY DIFFRACTION14chain 'C' and (resid 270 through 308 )
15X-RAY DIFFRACTION15chain 'C' and (resid 309 through 327 )
16X-RAY DIFFRACTION16chain 'D' and (resid 4 through 11 )
17X-RAY DIFFRACTION17chain 'D' and (resid 12 through 37 )
18X-RAY DIFFRACTION18chain 'D' and (resid 38 through 56 )
19X-RAY DIFFRACTION19chain 'D' and (resid 57 through 66 )
20X-RAY DIFFRACTION20chain 'D' and (resid 67 through 74 )
21X-RAY DIFFRACTION21chain 'D' and (resid 75 through 126 )
22X-RAY DIFFRACTION22chain 'D' and (resid 127 through 172 )

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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

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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

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