[English] 日本語
Yorodumi
- PDB-2jjt: Structure of human CD47 in complex with human signal regulatory p... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jjt
TitleStructure of human CD47 in complex with human signal regulatory protein (SIRP) alpha
Components
  • LEUKOCYTE SURFACE ANTIGEN CD47
  • TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE SUBSTRATE 1
KeywordsCELL ADHESION / SIGNAL REGULATORY PROTEIN ALPHA / IMMUNOGLOBULIN SUPERFAMILY / TRANSMEMBRANE / PHOSPHOPROTEIN / PAIRED RECEPTOR / POLYMORPHISM / GLYCOPROTEIN / PYRROLIDONE CARBOXYLIC ACID / ALTERNATIVE SPLICING / IMMUNOGLOBULIN DOMAIN / SIRP / CD47 / SIRPA / MEMBRANE / SH3-BINDING
Function / homology
Function and homology information


negative regulation of I-kappaB phosphorylation / cellular response to interleukin-12 / monocyte extravasation / regulation of Fc receptor mediated stimulatory signaling pathway / negative regulation of macrophage inflammatory protein 1 alpha production / negative regulation of chemokine (C-C motif) ligand 5 production / protein binding involved in heterotypic cell-cell adhesion / positive regulation of monocyte extravasation / regulation of interleukin-1 beta production / regulation of type II interferon production ...negative regulation of I-kappaB phosphorylation / cellular response to interleukin-12 / monocyte extravasation / regulation of Fc receptor mediated stimulatory signaling pathway / negative regulation of macrophage inflammatory protein 1 alpha production / negative regulation of chemokine (C-C motif) ligand 5 production / protein binding involved in heterotypic cell-cell adhesion / positive regulation of monocyte extravasation / regulation of interleukin-1 beta production / regulation of type II interferon production / cell-cell adhesion mediator activity / ATP export / GTPase regulator activity / positive regulation of cell-cell adhesion / regulation of interleukin-10 production / protein antigen binding / negative regulation of nitric oxide biosynthetic process / negative regulation of interferon-beta production / negative regulation of JNK cascade / regulation of tumor necrosis factor production / regulation of interleukin-12 production / regulation of nitric oxide biosynthetic process / negative regulation of phagocytosis / regulation of interleukin-6 production / Signal regulatory protein family interactions / thrombospondin receptor activity / tertiary granule membrane / negative regulation of interleukin-6 production / ficolin-1-rich granule membrane / negative regulation of tumor necrosis factor production / negative regulation of cytokine production involved in inflammatory response / Integrin cell surface interactions / cellular response to interleukin-1 / specific granule membrane / positive regulation of phagocytosis / positive regulation of stress fiber assembly / protein tyrosine kinase binding / negative regulation of protein phosphorylation / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / negative regulation of ERK1 and ERK2 cascade / cellular response to hydrogen peroxide / negative regulation of inflammatory response / SH3 domain binding / positive regulation of inflammatory response / cellular response to type II interferon / positive regulation of T cell activation / cell migration / regulation of gene expression / protein phosphatase binding / angiogenesis / cellular response to lipopolysaccharide / cell adhesion / inflammatory response / apoptotic process / positive regulation of cell population proliferation / Neutrophil degranulation / cell surface / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Leukocyte surface antigen CD47 / CD47-like, transmembrane / CD47 immunoglobulin-like / Leukocyte surface antigen CD47, IgV / CD47 transmembrane region / CD47 immunoglobulin-like domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype ...Leukocyte surface antigen CD47 / CD47-like, transmembrane / CD47 immunoglobulin-like / Leukocyte surface antigen CD47, IgV / CD47 transmembrane region / CD47 immunoglobulin-like domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type substrate 1 / Leukocyte surface antigen CD47
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHatherley, D. / Graham, S.C. / Turner, J. / Harlos, K. / Stuart, D.I. / Barclay, A.N.
CitationJournal: Mol. Cell / Year: 2008
Title: Paired receptor specificity explained by structures of signal regulatory proteins alone and complexed with CD47.
Authors: Hatherley, D. / Graham, S.C. / Turner, J. / Harlos, K. / Stuart, D.I. / Barclay, A.N.
History
DepositionApr 22, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other / Structure summary
Category: citation / exptl_crystal_grow ...citation / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct / struct_biol / struct_conn
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct.title / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 2.0Mar 11, 2020Group: Data collection / Other / Polymer sequence / Category: chem_comp / entity_poly / pdbx_database_status
Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf
Revision 2.1Jul 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.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Dec 13, 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 / 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_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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE SUBSTRATE 1
B: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE SUBSTRATE 1
C: LEUKOCYTE SURFACE ANTIGEN CD47
D: LEUKOCYTE SURFACE ANTIGEN CD47
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,20310
Polymers56,8764
Non-polymers1,3276
Water77543
1
A: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE SUBSTRATE 1
C: LEUKOCYTE SURFACE ANTIGEN CD47
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1015
Polymers28,4382
Non-polymers6643
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-7.2 kcal/mol
Surface area14060 Å2
MethodPQS
2
B: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE SUBSTRATE 1
D: LEUKOCYTE SURFACE ANTIGEN CD47
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1015
Polymers28,4382
Non-polymers6643
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-7.7 kcal/mol
Surface area13940 Å2
MethodPQS
Unit cell
Length a, b, c (Å)53.620, 63.720, 123.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEULEULEU1AA4 - 234 - 23
211LEULEULEULEU1BB4 - 234 - 23
121HISHISTHRTHR3AA24 - 2624 - 26
221HISHISTHRTHR3BB24 - 2624 - 26
131VALVALPHEPHE1AA27 - 3927 - 39
231VALVALPHEPHE1BB27 - 3927 - 39
141LEULEUGLNGLN1AA48 - 5248 - 52
241LEULEUGLNGLN1BB48 - 5248 - 52
151ARGARGVALVAL1AA59 - 6059 - 60
251ARGARGVALVAL1BB59 - 6059 - 60
161THRTHRTHRTHR3AA61 - 6261 - 62
261THRTHRTHRTHR3BB61 - 6261 - 62
171VALVALTHRTHR1AA63 - 6763 - 67
271VALVALTHRTHR1BB63 - 6763 - 67
181LYSLYSLYSLYS3AA6868
281LYSLYSLYSLYS3BB6868
191ARGARGVALVAL1AA69 - 11369 - 113
291ARGARGVALVAL1BB69 - 11369 - 113
112PCAPCAGLUGLU1CC1 - 111 - 11
212PCAPCAGLUGLU1DD1 - 111 - 11
122PHEPHEVALVAL3CC12 - 1912 - 19
222PHEPHEVALVAL3DD12 - 1912 - 19
132VALVALALAALA1CC20 - 3020 - 30
232VALVALALAALA1DD20 - 3020 - 30
142GLNGLNASNASN3CC31 - 3231 - 32
242GLNGLNASNASN3DD31 - 3231 - 32
152THRTHRLEULEU1CC33 - 5433 - 54
252THRTHRLEULEU1DD33 - 5433 - 54
162ASNASNASNASN3CC5555
262ASNASNASNASN3DD5555
172LYSLYSASPASP1CC56 - 8356 - 83
272LYSLYSASPASP1DD56 - 8356 - 83
182LYSLYSLYSLYS3CC8484
282LYSLYSLYSLYS3DD8484
192SERSERGLYGLY1CC85 - 9285 - 92
292SERSERGLYGLY1DD85 - 9285 - 92
1102ASNASNASNASN3CC9393
2102ASNASNASNASN3DD9393
1112TYRTYRCYSCYS1CC94 - 9694 - 96
2112TYRTYRCYSCYS1DD94 - 9694 - 96
1122GLUGLUGLUGLU3CC9797
2122GLUGLUGLUGLU3DD9797
1132VALVALARGARG1CC98 - 11498 - 114
2132VALVALARGARG1DD98 - 11498 - 114

NCS ensembles :
ID
1
2

-
Components

#1: Protein TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE SUBSTRATE 1 / SIRP ALPHA / SHP SUBSTRATE 1 / SHPS-1 / INHIBITORY RECEPTOR SHPS-1 / SIGNAL REGULATORY PROTEIN ...SIRP ALPHA / SHP SUBSTRATE 1 / SHPS-1 / INHIBITORY RECEPTOR SHPS-1 / SIGNAL REGULATORY PROTEIN ALPHA-1 / SIRP-ALPHA-1 / SIRP-ALPHA-2 / SIRP-ALPHA- 3 / MYD-1 ANTIGEN / BRAIN IG-LIKE MOLECULE WITH TYROSINE- BASED ACTIVATION MOTIFS / BIT / MACROPHAGE FUSION RECEPTOR / P84 / CD172A ANTIGEN


Mass: 13919.563 Da / Num. of mol.: 2 / Fragment: N-TERMINAL ECTODOMAIN, RESIDUES 31-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PEE14 / Cell line (production host): CHO / Production host: CRICETULUS GRISEUS (Chinese hamster) / Variant (production host): LEC3.2.8.1 / References: UniProt: P78324
#2: Antibody LEUKOCYTE SURFACE ANTIGEN CD47 / CD47 / INTEGRIN-ASSOCIATED PROTEIN / IAP / ANTIGENIC SURFACE DETERMINANT PROTEIN OA3 / PROTEIN MER6


Mass: 14518.302 Da / Num. of mol.: 2
Fragment: IMMUNOGLOBULIN-SUPERFAMILY ECTODOMAIN, RESIDUES 19-136
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PEE14 / Cell line (production host): CHO / Production host: CRICETULUS GRISEUS (Chinese hamster) / Variant (production host): LEC3.2.8.1 / References: UniProt: Q08722
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN C, CYS 33 TO GLY ENGINEERED RESIDUE IN CHAIN D, CYS 33 TO GLY
Sequence detailsSIRP ALPHA (CHAINS A AND B) RESIDUE NUMBERING IS FOR THE MATURE PROTEIN (LACKING N-TERMINAL 30 ...SIRP ALPHA (CHAINS A AND B) RESIDUE NUMBERING IS FOR THE MATURE PROTEIN (LACKING N-TERMINAL 30 AMINO ACID SIGNAL SEQUENCE). C-TERMINAL PURIFICATION TAG (TRHHHHHH) IS ADDED. CD47 RESIDUE NUMBERING IS FOR MATURE PROTEIN (LACKING N- TERMINAL 18 AMINO ACID SIGNAL SEQUENCE). RESIDUE 1 (GLN) CYCLISES TO FORM A PYROGLUTAMIC ACID. RESIDUE 15 WAS MUTATED FROM CYS TO GLY. C-TERMINAL PURIFICATION TAG ( STRHHHHHH) IS ADDED.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 33.4 % / Description: NONE
Crystal growTemperature: 278 K / pH: 5
Details: 100 NL SIRP ALPHA / CD47 COMPLEX (1:1 RATIO, EACH PROTEIN AT APPROX. 0.375 UM) PLUS 100 NL RESERVOIR (0.1 M CITRATE PH 5.0, 30% W/V PEG 3000) EQUILIBRATED AGAINST 95 UL OF RESERVOIR AT 5 C.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 4, 2006 / Details: MIRRORS
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 19339 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 7.4
Reflection shellResolution: 2.3→2.45 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.9 / % possible all: 98.5

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JJS CHAINS A AND C

2jjs


Resolution: 2.3→26.81 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.875 / SU B: 22.284 / SU ML: 0.256 / Cross valid method: THROUGHOUT / ESU R: 0.542 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. B VALUES INCLUDE TLS CONTRIBUTIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.288 989 5.1 %RANDOM
Rwork0.235 ---
obs0.238 18293 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.62 Å20 Å20 Å2
2--4.4 Å20 Å2
3----1.78 Å2
Refinement stepCycle: LAST / Resolution: 2.3→26.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3506 0 84 43 3633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223667
X-RAY DIFFRACTIONr_bond_other_d0.0040.022439
X-RAY DIFFRACTIONr_angle_refined_deg1.1931.9864985
X-RAY DIFFRACTIONr_angle_other_deg0.8213.0035947
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5645453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.08124.828145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74915605
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2031514
X-RAY DIFFRACTIONr_chiral_restr0.0740.2595
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024097
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02697
X-RAY DIFFRACTIONr_nbd_refined0.1680.2507
X-RAY DIFFRACTIONr_nbd_other0.1940.22313
X-RAY DIFFRACTIONr_nbtor_refined0.170.21699
X-RAY DIFFRACTIONr_nbtor_other0.0910.21955
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2107
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1330.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2760.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3221.52457
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.46523689
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.84231532
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.2664.51296
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1169tight positional0.030.05
2C1401tight positional0.030.05
1A40loose positional0.835
2C91loose positional1.445
1A1169tight thermal0.050.5
2C1401tight thermal0.060.5
1A40loose thermal0.6410
2C91loose thermal0.6410
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.35 59
Rwork0.292 1306
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)
13.03271.5186-1.82083.02921.22155.4104-0.0211-0.33480.05410.16990.236-0.06040.24460.1196-0.2149-0.14260.0581-0.01330.0147-0.0787-0.0909-4.0757-16.1226-38.2919
25.7643-0.55-2.43542.6731-0.67595.3597-0.30860.7178-0.4818-0.11370.2465-0.19260.422-0.15620.0621-0.1052-0.06040.0457-0.0266-0.0713-0.093713.8602-14.8264-21.9409
36.3671-0.5627-0.68660.93140.2442.0994-0.0618-0.0893-0.0078-0.0287-0.0224-0.0454-0.01340.40010.0843-0.0922-0.05850.0308-0.0396-0.0352-0.101420.267-12.713-50.1739
44.61330.9536-0.94211.2348-0.54433.2757-0.11020.3007-0.00110.00950.06440.13520.2217-0.29650.0459-0.10820.00820.0222-0.20330.0138-0.1582-9.8945-10.6325-10.3089
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 115
2X-RAY DIFFRACTION2B2 - 115
3X-RAY DIFFRACTION3C1 - 115
4X-RAY DIFFRACTION4D1 - 115

+
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