[English] 日本語
Yorodumi
- PDB-6ysq: The hC4Nb8 complement inhibitory nanobody in complex with C4b -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ysq
TitleThe hC4Nb8 complement inhibitory nanobody in complex with C4b
Components
  • Complement C4 beta chain
  • Complement C4 gamma chain
  • Complement C4-A alpha chain
  • hC4Nb8 nanobody
KeywordsIMMUNE SYSTEM / Nanobody / inhibitor / complement C4b
Function / homology
Function and homology information


detection of molecule of bacterial origin / classical-complement-pathway C3/C5 convertase complex / positive regulation of opsonization / opsonization / complement component C1q complex binding / symbiont cell surface / complement binding / positive regulation of apoptotic cell clearance / Activation of C3 and C5 / complement activation ...detection of molecule of bacterial origin / classical-complement-pathway C3/C5 convertase complex / positive regulation of opsonization / opsonization / complement component C1q complex binding / symbiont cell surface / complement binding / positive regulation of apoptotic cell clearance / Activation of C3 and C5 / complement activation / endopeptidase inhibitor activity / Initial triggering of complement / complement activation, classical pathway / Regulation of Complement cascade / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of immune response / carbohydrate binding / blood microparticle / inflammatory response / axon / endoplasmic reticulum lumen / innate immune response / neuronal cell body / dendrite / synapse / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Complement C4, MG1 domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / : / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin/fibulin / Anaphylatoxin, complement system ...: / Complement C4, MG1 domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / : / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin/fibulin / Anaphylatoxin, complement system / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor binding domain / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Immunoglobulin-like fold
Similarity search - Domain/homology
Complement C4-A / Complement C4-B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsZarantonello, A. / Laursen, N.S. / Andersen, G.R.
Funding support Denmark, 1items
OrganizationGrant numberCountry
LundbeckfondenR155-2015-2666 Denmark
CitationJournal: J Immunol. / Year: 2020
Title: An Ultrahigh-Affinity Complement C4b-Specific Nanobody Inhibits In Vivo Assembly of the Classical Pathway Proconvertase.
Authors: Zarantonello, A. / Presumey, J. / Simoni, L. / Yalcin, E. / Fox, R. / Hansen, A. / Olesen, H.G. / Thiel, S. / Johnson, M.B. / Stevens, B. / Laursen, N.S. / Carroll, M.C. / Andersen, G.R.
History
DepositionApr 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / struct_asym / struct_conn
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 19, 2020Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 3.0May 5, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / entity_src_nat / pdbx_branch_scheme / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_poly_seq_scheme / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_auth_evidence / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_residues / pdbx_validate_peptide_omega / pdbx_validate_torsion / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ncs_dom_lim / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.auth_asym_id / _atom_site.label_asym_id ..._atom_site.auth_asym_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_seq_id / _entity_src_gen.entity_id / _pdbx_branch_scheme.asym_id / _pdbx_branch_scheme.entity_id / _pdbx_branch_scheme.pdb_asym_id / _pdbx_entity_branch.entity_id / _pdbx_entity_branch_descriptor.entity_id / _pdbx_entity_branch_link.entity_id / _pdbx_entity_branch_list.entity_id / _pdbx_refine_tls_group.beg_auth_asym_id / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_refine_tls_group.selection_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_auth_evidence.details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_peptide_omega.auth_asym_id_1 / _pdbx_validate_peptide_omega.auth_asym_id_2 / _pdbx_validate_torsion.auth_asym_id / _struct_conf.beg_auth_asym_id / _struct_conf.beg_label_asym_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_label_asym_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_mon_prot_cis.label_asym_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_asym_id_2 / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_label_asym_id / _struct_sheet_range.end_label_seq_id
Revision 3.1Jan 24, 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Complement C4 beta chain
C: Complement C4-A alpha chain
E: Complement C4 gamma chain
B: Complement C4 beta chain
D: Complement C4-A alpha chain
F: Complement C4 gamma chain
G: hC4Nb8 nanobody
H: hC4Nb8 nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)392,42712
Polymers390,0818
Non-polymers2,3464
Water0
1
A: Complement C4 beta chain
C: Complement C4-A alpha chain
E: Complement C4 gamma chain
G: hC4Nb8 nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,2146
Polymers195,0404
Non-polymers1,1732
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Complement C4 beta chain
D: Complement C4-A alpha chain
F: Complement C4 gamma chain
H: hC4Nb8 nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,2146
Polymers195,0404
Non-polymers1,1732
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.200, 89.510, 231.200
Angle α, β, γ (deg.)90.000, 97.552, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSCYSCYSAA20 - 6691 - 650
121ALAALATYRTYRCB757 - 12291 - 473
131GLNGLNALAALACB1256 - 1413500 - 657
141GLNGLNARGARGEC1462 - 16049 - 151
151GLYGLYVALVALEC1611 - 1744158 - 291
161NAGNAGBMABMAII1 - 3
1151NAGNAGBMABMAJJ1 - 3
271LYSLYSCYSCYSBD20 - 6691 - 650
281ALAALATYRTYRDE757 - 12291 - 473
291GLNGLNALAALADE1256 - 1413500 - 657
2101GLNGLNARGARGFF1462 - 16049 - 151
2111GLYGLYVALVALFF1611 - 1744158 - 291
2121NAGNAGBMABMAKK1 - 3
2161NAGNAGBMABMALL1 - 3
1132GLNGLNSERSERGG1 - 1231 - 123
2142GLNGLNSERSERHH1 - 1231 - 123

NCS ensembles :
ID
1
2

-
Components

#1: Protein Complement C4 beta chain


Mass: 71761.688 Da / Num. of mol.: 2
Fragment: Acidic complement C4,C3 and PZP-like alpha-2-macroglobulin domain-containing protein 2
Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P0C0L4, UniProt: P0C0L5*PLUS
#2: Protein Complement C4-A alpha chain


Mass: 75509.922 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P0C0L4
#3: Protein Complement C4 gamma chain


Mass: 33085.602 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P0C0L5
#4: Antibody hC4Nb8 nanobody


Mass: 14683.265 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#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.: 4
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
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.36 Å3/Da / Density % sol: 63.44 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: The reservoir containing 100 mM HEPES-NaOH pH=7, 10% w/w PEG4000, 10% v/v 2-propanol was mixed 1:1 with the concentrated protein sample.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3.3→48.26 Å / Num. obs: 80517 / % possible obs: 99.87 % / Redundancy: 6.7 % / Biso Wilson estimate: 147.97 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.73
Reflection shellResolution: 3.3→3.418 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 0.65 / Num. unique obs: 7914 / CC1/2: 0.341 / % possible all: 99.94

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JTW

5jtw


Resolution: 3.3→48.26 Å / SU ML: 0.5986 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.0822
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2718 1566 1.95 %
Rwork0.2206 78887 -
obs0.2216 80453 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 195.32 Å2
Refinement stepCycle: LAST / Resolution: 3.3→48.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26297 0 0 0 26297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004626860
X-RAY DIFFRACTIONf_angle_d0.929136442
X-RAY DIFFRACTIONf_chiral_restr0.0584100
X-RAY DIFFRACTIONf_plane_restr0.00864733
X-RAY DIFFRACTIONf_dihedral_angle_d8.327816126
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.410.41761400.37477063X-RAY DIFFRACTION99.92
3.41-3.530.43311420.3537143X-RAY DIFFRACTION99.97
3.53-3.670.38591420.33577097X-RAY DIFFRACTION99.97
3.67-3.840.37011410.30587139X-RAY DIFFRACTION100
3.84-4.040.34251420.27687159X-RAY DIFFRACTION99.99
4.04-4.290.27241420.24857159X-RAY DIFFRACTION99.97
4.29-4.620.28321420.21687139X-RAY DIFFRACTION100
4.62-5.090.2581420.19777166X-RAY DIFFRACTION100
5.09-5.820.27131430.21147215X-RAY DIFFRACTION99.93
5.82-7.330.30031440.23267248X-RAY DIFFRACTION100
7.33-48.260.20161460.17117359X-RAY DIFFRACTION99.3
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)
15.809485043230.2018179102520.8345843508686.61937101343-1.123544988274.991095057950.006909107288950.0461623903581.06590366506-0.337265646804-0.0429981550136-0.140859586761-0.6346793326230.1422926947490.03013866165491.61700426455-0.1778792063260.02063496494170.7552289023320.06033538634631.02881979895-23.401890339940.0867549193-77.4890585659
25.84187251605-3.530590480823.419605297748.95018721814-5.970613647118.95162453446-0.2439986132860.55486068498-0.254288434449-0.054139237830.043467697831-0.2703634714030.0836813930717-0.01287254135680.1705317285761.12121288905-0.07215311580880.1678297605810.82067881033-0.1717639000790.765151860512-24.27649709089.27022170964-54.0197124424
37.965360139731.28619775447-0.8429970905023.06961533535-2.189369623941.569033927040.500559858327-0.7137378737420.282976111042-0.341123839916-0.758880542455-0.3963809550220.1533178163161.390468794480.2629983618020.969035239961-0.02093215085760.04064666382492.060343977730.3090813787311.5739857042210.24626947211.71141211504-40.4168150885
44.854665148711.28402582281-1.43709967226.29710460305-2.727338406283.90262721517-0.3315514168420.1094257886840.471125733651-0.00225824654677-0.136673037166-1.30674837129-1.009302731091.419387601280.3430827480741.29913100252-0.494919051060.01603361328381.817743157940.4713160424912.1122021133914.084709704333.8670798711-59.6759956074
54.74301351261.64716213175-1.70078053435.34028529168-4.487900892586.77738335347-0.544242047418-0.2128049748451.74902549594-0.215683997692-0.491321931002-0.0679374244419-0.7529050746741.185928770870.9881372521761.78659044496-0.63282534781-0.07238596373451.144125090790.02038071359071.86402743605-6.2443027604346.1390324932-61.6146414842
61.78729160628-2.905261657322.793315121228.63759022812-5.199520196077.03471927441-0.329474601137-0.517393712990.26046087350.2400356612610.170184845008-0.469991630484-0.478270630845-0.6666708344490.2088017630231.19911337022-0.330375305571-0.005489716346671.29153743167-0.2287929960991.02227719562-21.662793981911.3055523108-28.237407733
7-0.1487912241212.73255918333-2.521011486945.25746759447-7.188313483918.081281926990.05837148575-0.3024154297940.0401708844942-1.10396718524-0.593788345885-0.659210046130.797465618750.9957292836530.8426389533761.27550820832-0.07307293196580.231090826441.568762569580.2604991937811.54655173287-9.1800958697627.012096972-63.8433114695
85.9893783753-0.505392228254-0.9305403817138.68031445423-1.676487904394.5842303069-0.1899388222420.008424678162020.0211617611094-0.411607236653-0.441202291233-0.3027807125370.1256275231991.654991808430.6506125807770.849493268196-0.1456675340560.008718753746291.174088008690.1179073434880.956608127449-15.4606650731-13.0851703248-22.5477729572
92.69150546623-2.224105051031.185824320727.83793462797-6.548413995928.4148814370.2456374767560.188134656907-0.535568169107-1.65204825231-0.1372462462070.8177233258521.901244210850.00857889045556-0.2473917818842.0183956898-0.2435740352010.07256378010210.990193443943-0.23030566611.32713578206-27.4316917356-13.3200492759-65.8811901415
101.273777039390.724311918223-0.9432573844393.41791109317-1.142884779023.16277035246-0.1995669206380.403374199241-0.290362797936-1.042406909040.04966486692360.415307982691.129689312440.04012762411340.1187795700032.87716058898-0.05269884510570.2495943058251.0900846068-0.06650178623591.28005987979-26.449827541921.579591481-107.576676433
1110.0236876431-2.575840135480.3076285477874.908052838321.2798090840910.3303935361-0.034119453049-1.8869374859-0.002939529293151.184826922750.005088700599420.55180405987-0.3157644166-0.8351287365820.01282300893711.01393791945-0.238933759830.1533144521271.66327068183-0.07475025279220.889724956275-41.53780184687.98037220926-17.0831400177
126.201048030393.221879703490.8223698079678.39768254252-1.305485144123.6159232849-0.347483531152-0.3330704515080.98337488562-0.8964266626130.03172069139670.4674436014630.0854785869327-0.1896642593260.327798287171.910346812090.171021568397-0.3302642093260.982382211638-0.05913311956811.03793987249-83.11665082840.1765147984-77.8070489238
135.15438998029-1.448523927530.2644755330287.27219880764-4.692261143159.24659216446-0.01058891245180.345276564269-0.1492002340230.06552589265670.1134697709830.5628659110390.167679556438-0.688740414887-0.1329109996951.24091589664-0.06536917936310.08787224875921.06257077225-0.1934261828350.901979495955-86.72352585679.32010753505-54.7973877029
148.186263521992.6472304881-3.401718829217.05903800581-0.863294976454.339396877630.304491031788-0.7613173160430.445371704783-0.355961082256-0.14156356456-0.143101285629-0.1348932173850.451208186367-0.182767127150.719242236304-0.122324812459-0.1326530009331.04503622513-0.08011918644980.74912466708-54.11085650951.46397840532-37.9429464306
153.349618375552.22451825446-0.7965858374138.10149273655-5.219362906117.20538381218-0.124334305768-0.4621894616760.08691995641990.4647309017620.2071506117160.00545316861266-1.077834030630.0120718876984-0.170887635041.347414102790.07967283716580.2125451113370.756172281879-0.05080993654941.31847323381-48.188740175734.1835705328-55.4195905465
169.823000588671.45668032782-3.714173111755.72221241302-3.069018552839.31388583113-0.213091720683-0.2470990202331.34715932918-0.653058789862-0.07218894542230.717016498745-0.3501018035040.2126538349480.2753707990311.481084756870.0263420205661-0.1192344031490.728059790384-0.279379454061.3846864339-67.839982208746.2829360131-60.2590607273
171.1414213301-1.72345439672.366453696375.48169272824-5.673088661187.20593583042-0.496494463774-0.402235535120.01199356388010.6679393654840.341051728406-0.130876279319-0.616355476424-1.009826044820.1526687090630.998874383445-0.08399799130730.1173500743751.24019856265-0.3091903852121.01512179485-86.855749355210.9077029333-28.8903366898
180.390447928873.02740166599-2.54998440594.65742174351-4.76865344485.10021871992-0.0803818281026-0.3463552083040.1628049067-1.44722712759-0.495012615567-0.3770188312470.6945113401730.1520004016350.7563974564341.403265728450.159256208997-0.04846067381461.283802649060.1762944002571.34337145419-70.507556050727.120189682-62.7276384981
196.234331503693.155211895454.755192271969.231306889662.4853678676210.0301427315-0.239825974549-0.441520389349-0.491842984273-0.07097087636390.278277377102-0.0240464661958-0.5891192562451.05450125882-0.05161851892350.82702497048-0.2129372370750.1592542508881.21312002430.0896546398730.951194341223-81.4701049297-13.7150022992-23.1174490442
204.16963941524-3.275140552472.822174893757.05528189979-4.163753682393.568771535520.1772695615890.174795213062-0.59086191728-2.324025992-0.04178741437160.7441943058821.41221929822-0.0377794603434-0.1552347135522.528035583-0.5157331650760.001831642523651.25062951331-0.2583228341131.38943366795-88.87890577-13.0722282923-67.0765643792
212.36389461967-1.16430346676-1.172786429524.522373425080.3216725704033.35993351861-0.4181170701540.646738805441-0.276759656694-2.096903524750.405914552397-0.1916144965560.9241617273860.1752137490190.03478239403093.57923545185-0.2424271509620.09425071930971.204034950170.0326159573191.34292854132-82.830044987421.374088587-107.861963873
226.51860341782-2.62133849948-1.339820870574.892373654750.4986104332586.95884137731-0.478763169024-0.783931632819-0.5194023033640.6595909339980.2654492215531.322331973380.109872606083-0.5924699860620.1923676700880.749714278033-0.1650652635080.1883688224151.69732250072-0.1057198912841.33841126207-107.7679298527.63389729067-19.9878814048
238.468005190386.37587688551-1.369037989729.44066203113-3.898951261692.12180032789-0.883822134731-0.588203985124-0.4412772979140.4178172176920.3736668864350.5078501622540.852738184544-0.5824462609920.5508991835382.16636813911-0.03639133910670.6041715099841.27076161537-0.2962378336951.88076309153-33.1576313375-43.4263495937-22.2134993365
248.224957626296.881128767130.08170626235325.72011937264-0.192294590444.42029977177-0.532029066467-0.284436921592-0.780850718976-0.04161593648090.34594172384-0.933987607811-0.331870321287-0.5427339618970.1541319674311.458230850960.1662039497590.3323529206811.031805602640.05454439039952.01234096748-99.2326287573-43.7022827983-24.3294167262
254.345459520714.4418577619-3.188680628378.43721891456-0.332204941813.15004591129-0.1570874564640.0830005110933-0.12093514622-0.222606530666-0.718613074894-0.6689746208531.207568912011.758685003280.7178698232781.161491946020.640037991370.05467614374762.780828697070.7712120413661.53391219394.54177001094-21.5870259943-26.9949576571
265.300395650155.37194466621-6.065329036039.12945596919-3.955752773267.88147865756-0.336345464133-0.0278563697405-0.517021566313-0.4562627624530.0859613950478-0.02203303954970.7099929035380.07763813191940.2821347288010.8751473916930.157389545984-0.04027427257582.180228866120.2449177062831.60037704636-61.2399985539-22.3299872219-26.1631549566
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-IDSelection details
1X-RAY DIFFRACTION1A20 - 139
2X-RAY DIFFRACTION2A140 - 236
3X-RAY DIFFRACTION3A237 - 361
4X-RAY DIFFRACTION4A362 - 468
5X-RAY DIFFRACTION5A469 - 568
6X-RAY DIFFRACTION6A569 - 605
7X-RAY DIFFRACTION7A606 - 670
8X-RAY DIFFRACTION8C832 - 934
9X-RAY DIFFRACTION9(resid 935:982 or resid 1321:1392) and chain C
10X-RAY DIFFRACTION10C983 - 1320
11X-RAY DIFFRACTION11G1 - 132
12X-RAY DIFFRACTION12B20 - 139
13X-RAY DIFFRACTION13B140 - 236
14X-RAY DIFFRACTION14B237 - 361
15X-RAY DIFFRACTION15B362 - 468
16X-RAY DIFFRACTION16B469 - 568
17X-RAY DIFFRACTION17B569 - 605
18X-RAY DIFFRACTION18B606 - 670
19X-RAY DIFFRACTION19D832 - 934
20X-RAY DIFFRACTION20(resid 935:982 or resid 1321:1392) and chain D
21X-RAY DIFFRACTION21D983 - 1320
22X-RAY DIFFRACTION22H1 - 132
23X-RAY DIFFRACTION23E1574 - 1744
24X-RAY DIFFRACTION24F1574 - 1744
25X-RAY DIFFRACTION25(resid 1393:1414 and chain C) and (resid 1462:1573 and chain E)
26X-RAY DIFFRACTION26(resid 1393:1414 and chain D) and (resid 1462:1573 and chain F)

+
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