[English] 日本語
Yorodumi
- PDB-6lzg: Structure of novel coronavirus spike receptor-binding domain comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lzg
TitleStructure of novel coronavirus spike receptor-binding domain complexed with its receptor ACE2
Components
  • Angiotensin-converting enzyme 2
  • Spike protein S1
KeywordsVIRAL PROTEIN / Novel Coronavirus / Spike protein / receptor
Function / homology
Function and homology information


positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / positive regulation of gap junction assembly / regulation of cardiac conduction / regulation of vasoconstriction ...positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / positive regulation of gap junction assembly / regulation of cardiac conduction / regulation of vasoconstriction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / negative regulation of signaling receptor activity / carboxypeptidase activity / Attachment and Entry / positive regulation of cardiac muscle contraction / viral life cycle / regulation of cytokine production / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / brush border membrane / regulation of transmembrane transporter activity / cilium / negative regulation of ERK1 and ERK2 cascade / metallopeptidase activity / positive regulation of reactive oxygen species metabolic process / endocytic vesicle membrane / virus receptor activity / regulation of cell population proliferation / regulation of inflammatory response / endopeptidase activity / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Potential therapeutics for SARS / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / membrane raft / apical plasma membrane / endoplasmic reticulum lumen / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / cell surface / extracellular space / extracellular exosome / zinc ion binding / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / Neutral zinc metallopeptidases, zinc-binding region signature. / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal ...Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / Neutral zinc metallopeptidases, zinc-binding region signature. / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Spike glycoprotein / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWang, Q.H. / Song, H. / Qi, J.X.
CitationJournal: Cell / Year: 2020
Title: Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2.
Authors: Wang, Q. / Zhang, Y. / Wu, L. / Niu, S. / Song, C. / Zhang, Z. / Lu, G. / Qiao, C. / Hu, Y. / Yuen, K.Y. / Wang, Q. / Zhou, H. / Yan, J. / Qi, J.
History
DepositionFeb 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Structure summary / Category: entity / Item: _entity.pdbx_description
Revision 2.0Apr 22, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Database references / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / citation_author / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_instance_feature / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_unobs_or_zero_occ_residues / refine / refine_ls_restr / refine_ls_shell / software / struct_ref / struct_ref_seq
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _software.version / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Description: Model orientation/position / Provider: author / Type: Coordinate replacement
Revision 2.1May 6, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 2.2May 27, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.4Mar 10, 2021Group: Structure summary / Category: chem_comp / entity / entity_name_com
Item: _chem_comp.pdbx_synonyms / _entity.pdbx_description / _entity_name_com.name
Revision 2.5Nov 29, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Angiotensin-converting enzyme 2
B: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,5027
Polymers92,5522
Non-polymers9505
Water5,801322
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-23 kcal/mol
Surface area34880 Å2
Unit cell
Length a, b, c (Å)104.448, 104.448, 229.786
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

#1: Protein Angiotensin-converting enzyme 2 / ACE-related carboxypeptidase / Angiotensin-converting enzyme homolog / ACEH / Metalloprotease MPROT15


Mass: 69038.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACE2, UNQ868/PRO1885
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q9BYF1, angiotensin-converting enzyme 2, Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases
#2: Protein Spike protein S1 / S glycoprotein / E2 / Peplomer protein / Spike glycoprotein


Mass: 23513.389 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: P0DTC2
#3: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES pH 6.5,10%w/v PEG 5000 MME,12% v/v 1-propanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97919 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 44981 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 21.6 % / Biso Wilson estimate: 35.62 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.129 / Net I/σ(I): 26.7
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 22.3 % / Mean I/σ(I) obs: 3.3 / Num. unique obs: 4384 / CC1/2: 0.867 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data processing
PHASERphasing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ajf

2ajf


Resolution: 2.5→34.5 Å / SU ML: 0.2505 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.6451
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2156 2304 5.14 %
Rwork0.1884 42557 -
obs0.1898 44861 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.01 Å2
Refinement stepCycle: LAST / Resolution: 2.5→34.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6405 0 57 322 6784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00546649
X-RAY DIFFRACTIONf_angle_d0.82989040
X-RAY DIFFRACTIONf_chiral_restr0.2842957
X-RAY DIFFRACTIONf_plane_restr0.00511173
X-RAY DIFFRACTIONf_dihedral_angle_d23.90622428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.550.23691030.25112617X-RAY DIFFRACTION98.69
2.55-2.610.2991420.23432598X-RAY DIFFRACTION100
2.61-2.680.241510.21812618X-RAY DIFFRACTION100
2.68-2.750.24861520.21642608X-RAY DIFFRACTION100
2.75-2.830.271310.21172612X-RAY DIFFRACTION100
2.83-2.920.2441500.21962619X-RAY DIFFRACTION100
2.92-3.030.24341450.20912623X-RAY DIFFRACTION100
3.03-3.150.26291230.20782669X-RAY DIFFRACTION100
3.15-3.290.23661400.20812642X-RAY DIFFRACTION100
3.29-3.460.23071350.19342642X-RAY DIFFRACTION100
3.46-3.680.21051540.18462647X-RAY DIFFRACTION100
3.68-3.960.23891260.16832690X-RAY DIFFRACTION100
3.96-4.360.17521490.1592691X-RAY DIFFRACTION100
4.36-4.990.17411670.14992678X-RAY DIFFRACTION100
4.99-6.280.21981630.17852725X-RAY DIFFRACTION100
6.28-34.50.17621730.18712878X-RAY DIFFRACTION99.41
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)
10.715851578218-0.154721369542-0.2801042550682.925480296150.2666386140451.370729247150.07229950140370.1439275179590.06997567979760.04442626267840.02981603343780.615512083351-0.237659428587-0.260228196461-0.002186580815880.3148805147140.06085670667570.0710310626380.4283819372160.01360456389870.435901516712-40.264207696225.9052284911-7.12159673486
20.0685148145115-0.027836569305-0.03793071457530.0532562033081-0.1625015363710.874236892887-0.00793154805256-0.09102101561750.109415687688-0.0813949686983-0.02803809637770.170806647181-0.361886627404-0.124728634574-0.02653486849840.2806773639730.01291595689710.0597699087160.360620706815-0.04125951779020.383049449778-37.636820387633.4168026782-20.6939129259
31.0556755778-0.844342794357-0.3553713465950.782052655034-0.103549085651.52973415717-0.0007445414784940.120083458698-0.18604329735-0.125896027886-0.04967869896590.5838773106610.134520181638-0.3125745124950.04666680441020.169900557741-0.0579965651246-0.0343075523140.277551250022-0.02979214909590.339629412766-39.177778093311.6544040819-40.1053030872
40.83424517063-0.283246505933-0.407441225721.132512228070.4966228537761.395640300610.00797890211550.0143942547490.0357993513693-0.1021946354860.0154525924774-0.0194054335224-0.03962720097210.112896454013-0.06311430806530.193984335413-0.03913635688350.01292367575840.251237779872-0.01157017585970.2167998996-18.737244074215.7175186278-35.9795825191
50.641731780615-0.0387068452731-0.2231660189862.330791230030.1164407578081.44140944788-0.0605121026563-0.12694812162-0.09093022932650.06370917353670.08938657770360.1189382216130.2671600920590.09924967938720.001229411395020.2106505721810.03700965769790.01346256967040.26541117691-0.006223008720690.202635448836-22.34563868895.4821477869-11.3024484569
60.680056622261-0.2127735076690.142535517510.844874525720.123237418481.55368290954-0.0181722644122-0.01697583493940.0615798502772-0.03205129067140.0521257348951-0.0880418974382-0.02351099269580.19400975714-0.04615892598420.1884659565-0.02433697051490.03058148655490.269160383344-0.00879626158210.244060953926-17.337554009316.8565602627-32.113966184
70.9376970962830.319657814436-0.1456737274210.5218617697440.5714206656221.41526375981-0.238020696114-0.620641224194-0.25805315970.4953128349760.161164862264-0.0846149458670.414559298040.154871625035-0.03985170262270.5052857902710.1261701910680.01797709947560.5743006637660.05286011577180.291761022289-36.550072225720.862741860630.7792845293
81.143177005990.0851754041685-0.9406589582670.0361316510435-0.3308685856063.89028894534-0.0600774589822-0.601197057017-0.5747086046970.603205415345-0.11132539691-0.3654563993020.6081376909960.3822878212310.03844643731160.5774337653750.1496690593-0.02754728194740.7552765526740.1243109349920.623052475769-23.663285512114.4235747626.9633193757
90.00160714773989-0.05920530963710.0345255178422.19014694179-1.251642277780.722905442778-0.406473626551-0.385481884352-0.3664989132410.1483289344430.0833055741723-0.4365453830180.4181384085050.694364359750.03639856031430.8474392222870.260051635621-0.2031998330221.39234733817-0.08966266819740.827711489467-20.243289947519.602883719637.6787450642
101.33729826853-0.308171288114-0.2925171512921.38073281921-0.1369269396441.1187360840.00119727589103-0.185698348893-0.06272680156690.09460423293640.0719065802416-0.201811365186-0.08589308685260.269462209534-0.06043194563190.3051974975420.008172711439410.04216382819110.440370881693-0.01998899768570.323712076851-31.380354995326.315109301716.8885215757
111.12493444192-0.223718857207-0.1927719032220.814442812762-0.2404583168161.797436550190.167695685606-0.04686991688570.4650173062320.1725632496430.01669540842290.181215587349-0.500173106423-0.0785996042557-0.1057680230070.4865226488150.02433409752480.09912354842130.4504344747450.004934318421930.4532281313-39.527903907140.799308568110.0840123775
120.590022126031-0.0731587571597-0.8012557669642.223849993971.139270219521.57620974938-0.0273780436430.1158257827320.0958884143619-0.008014285293140.1144937275230.120200583976-0.0263076393792-0.005094587989610.03478700357340.2924308927990.04155269897580.08605157659410.364925291320.02008326125340.277248219471-34.950392391617.30971156425.94610477428
132.02103163130.100660217532-0.1328153091961.81938369623-0.04822253714062.01773936063-0.128034343685-0.7878349703980.1018315742850.6730905119390.132086723752-0.320009649157-0.09737447658390.453996199514-0.06341102988320.4798878872640.0667060258956-0.1094986907020.736835026519-0.066434362830.402252476284-28.273820267124.266566296633.8684400335
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 82 )
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 129 )
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 193 )
4X-RAY DIFFRACTION4chain 'A' and (resid 194 through 293 )
5X-RAY DIFFRACTION5chain 'A' and (resid 294 through 431 )
6X-RAY DIFFRACTION6chain 'A' and (resid 432 through 614 )
7X-RAY DIFFRACTION7chain 'B' and (resid 333 through 364 )
8X-RAY DIFFRACTION8chain 'B' and (resid 365 through 380 )
9X-RAY DIFFRACTION9chain 'B' and (resid 381 through 393 )
10X-RAY DIFFRACTION10chain 'B' and (resid 394 through 459 )
11X-RAY DIFFRACTION11chain 'B' and (resid 460 through 494 )
12X-RAY DIFFRACTION12chain 'B' and (resid 495 through 506 )
13X-RAY DIFFRACTION13chain 'B' and (resid 507 through 527 )

+
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