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- PDB-6f1h: C1rC1s complex -

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Basic information

Entry
Database: PDB / ID: 6f1h
TitleC1rC1s complex
Components
  • Complement C1r subcomponent
  • Complement C1s subcomponent
KeywordsHYDROLASE / CUB domain / EGF-like domain / complement / C1r-C1s
Function / homology
Function and homology information


complement subcomponent C_overbar_1r_ / complement subcomponent C_overbar_1s_ / molecular sequestering activity / zymogen activation / Classical antibody-mediated complement activation / Initial triggering of complement / complement activation, classical pathway / serine-type peptidase activity / Regulation of Complement cascade / blood microparticle ...complement subcomponent C_overbar_1r_ / complement subcomponent C_overbar_1s_ / molecular sequestering activity / zymogen activation / Classical antibody-mediated complement activation / Initial triggering of complement / complement activation, classical pathway / serine-type peptidase activity / Regulation of Complement cascade / blood microparticle / immune response / serine-type endopeptidase activity / innate immune response / calcium ion binding / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Peptidase S1A, complement C1r/C1S/mannan-binding / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. ...Peptidase S1A, complement C1r/C1S/mannan-binding / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Coagulation Factor Xa inhibitory site / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain signature 2. / EGF-like domain / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
LYSINE / Complement C1r subcomponent / Complement C1s subcomponent
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.5 Å
AuthorsAlmitairi, J.O.M. / Venkatraman Girija, U. / Furze, C.M. / Simpson-Gray, X. / Badakshi, F. / Marshall, J.E. / Mitchell, D.A. / Moody, P.C.E. / Wallis, R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G1000191/1 United Kingdom
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structure of the C1r-C1s interaction of the C1 complex of complement activation.
Authors: Almitairi, J.O.M. / Venkatraman Girija, U. / Furze, C.M. / Simpson-Gray, X. / Badakshi, F. / Marshall, J.E. / Schwaeble, W.J. / Mitchell, D.A. / Moody, P.C.E. / Wallis, R.
History
DepositionNov 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _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_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Complement C1r subcomponent
C: Complement C1r subcomponent
D: Complement C1s subcomponent
B: Complement C1s subcomponent
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,77229
Polymers128,4734
Non-polymers5,29925
Water0
1
A: Complement C1r subcomponent
B: Complement C1s subcomponent
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,63014
Polymers64,2362
Non-polymers2,39312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-20 kcal/mol
Surface area30680 Å2
MethodPISA
2
C: Complement C1r subcomponent
D: Complement C1s subcomponent
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,14215
Polymers64,2362
Non-polymers2,90613
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-13 kcal/mol
Surface area31520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.209, 88.340, 197.559
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain B and (resid 2 through 157 or resid 159 through 276))
21(chain D and (resid 2 through 157 or resid 159 through 276))
12(chain A and (resid 4 through 9 or resid 11 through 291))
22chain C

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROGLYGLY(chain B and (resid 2 through 157 or resid 159 through 276))BD2 - 1571 - 156
121ASNASNPROPRO(chain B and (resid 2 through 157 or resid 159 through 276))BD159 - 276158 - 275
211PROPROGLYGLY(chain D and (resid 2 through 157 or resid 159 through 276))DC2 - 1571 - 156
221ASNASNPROPRO(chain D and (resid 2 through 157 or resid 159 through 276))DC159 - 276158 - 275
112ILEILEPHEPHE(chain A and (resid 4 through 9 or resid 11 through 291))AA4 - 94 - 9
122GLUGLULYSLYS(chain A and (resid 4 through 9 or resid 11 through 291))AA11 - 29111 - 291
212ILEILEILEILEchain CCB4 - 2904 - 290

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ACDB

#1: Protein Complement C1r subcomponent / Complement component 1 subcomponent r


Mass: 33120.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C1R / Plasmid: pED4 / Cell line (production host): DXB11 / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: P00736, complement subcomponent C_overbar_1r_
#2: Protein Complement C1s subcomponent / C1 esterase / Complement component 1 subcomponent s


Mass: 31115.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C1S / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: P09871, complement subcomponent C_overbar_1s_

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Sugars , 4 types, 6 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-galactopyranose-(1-4)-alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-galactopyranose-(1-4)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1276.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGalpb1-4DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5]/1-1-2-3-4-1-3/a4-b1_b4-c1_c3-d1_c6-g1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(4+1)][b-D-Galp]{[(4+1)][b-D-GlcpNAc]{}}}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1276.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5]/1-1-2-3-1-4-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#8: 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 , 3 types, 19 molecules

#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#9: Chemical ChemComp-LYS / LYSINE / Lysine


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2

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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 Å3/Da / Density % sol: 58.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 12-18% PEG 8000, 100 mM Imidazole at pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 4.5→88.3 Å / Num. obs: 9382 / % possible obs: 98.1 % / Redundancy: 5 % / Biso Wilson estimate: 154.99 Å2 / Rmerge(I) obs: 0.164 / Net I/σ(I): 5.4
Reflection shellResolution: 4.5→4.66 Å / Mean I/σ(I) obs: 1.9 / % possible all: 98.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXdev_2722refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LOR

4lor


Resolution: 4.5→80.645 Å / SU ML: 0.86 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 46.97
RfactorNum. reflection% reflection
Rfree0.3398 485 5.18 %
Rwork0.3035 --
obs0.3052 9358 97.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 404.11 Å2 / Biso mean: 255.4534 Å2 / Biso min: 169.57 Å2
Refinement stepCycle: final / Resolution: 4.5→80.645 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8988 0 330 0 9318
Biso mean--282.61 --
Num. residues----1128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039611
X-RAY DIFFRACTIONf_angle_d0.73413094
X-RAY DIFFRACTIONf_chiral_restr0.0521409
X-RAY DIFFRACTIONf_plane_restr0.0051700
X-RAY DIFFRACTIONf_dihedral_angle_d13.2095753
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B2629X-RAY DIFFRACTION6.644TORSIONAL
12D2629X-RAY DIFFRACTION6.644TORSIONAL
21A0X-RAY DIFFRACTION6.644TORSIONAL
22C0X-RAY DIFFRACTION6.644TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.5001-5.15120.41651650.37862877304298
5.1512-6.48950.38351530.36512954310797
6.4895-80.65760.31670.25713042320996
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)
1-0.6653-3.0246-1.07370.7649-0.11158.71770.09651.7167-0.7124-0.6178-0.4483-0.42050.3619-2.0112-0.00082.6312-0.41830.37432.9989-0.58023.097760.50711.031-31.5039
20.9419-1.39-0.27266.76670.7775.9309-0.05270.15170.01560.2782-0.43390.13510.5959-0.833901.8958-0.44570.27562.78-0.30362.180628.160216.251614.8169
36.9454-0.95760.80980.4002-1.42732.4941-0.507-2.3376-0.05631.00071.08310.20392.0650.6393-0.00263.409-1.0492-0.22052.8191-0.14542.0912.512-4.1497-2.1514
45.31611.7906-7.7051.6983-1.35179.6090.677-1.2120.9477-0.7880.16730.0486-0.9950.6308-0.00022.152-0.0206-0.2562.38590.08942.771142.6991-0.0375-53.1115
59.79691.255-1.67913.7738-1.42718.42210.88830.0238-0.03950.1073-0.41870.45060.0077-0.3412-0.00012.00960.2532-0.12312.33970.07861.924218.839-13.4962-42.23
64.69123.03341.68762.98394.61518.4208-0.7741-1.37720.4065-2.1266-0.49190.3173-1.5965-1.69330.0014.4815-1.393-0.0132.7266-0.18052.8053-11.9839-17.30257.0416
77.2474-3.4539-1.13945.14622.80030.47450.6431-0.4023-0.2156-1.8924-0.3353-0.2001-1.12280.85880.00031.88560.10550.16591.5673-0.12162.499161.017611.5442.0509
82.77381.85233.21269.0901-0.01744.3829-0.6958-0.44510.180.54930.763-0.84720.26381.59820.00013.36880.9130.35972.641-0.4773.131994.8229.0943-35.1942
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 165 )A1 - 165
2X-RAY DIFFRACTION2chain 'A' and (resid 166 through 293 )A166 - 293
3X-RAY DIFFRACTION3chain 'C' and (resid 4 through 125 )C4 - 125
4X-RAY DIFFRACTION4chain 'C' and (resid 126 through 291 )C126 - 291
5X-RAY DIFFRACTION5chain 'D' and (resid 2 through 142 )D2 - 142
6X-RAY DIFFRACTION6chain 'D' and (resid 143 through 276 )D143 - 276
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 142 )B2 - 142
8X-RAY DIFFRACTION8chain 'B' and (resid 143 through 277 )B143 - 277

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  • 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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