[English] 日本語
Yorodumi
- PDB-3b2u: Crystal structure of isolated domain III of the extracellular reg... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3b2u
TitleCrystal structure of isolated domain III of the extracellular region of the epidermal growth factor receptor in complex with the Fab fragment of IMC-11F8
Components
  • (IMC-11F8 Fab ...) x 2
  • Epidermal growth factor receptor
KeywordsIMMUNE SYSTEM/TRANSFERASE / CELL SURFACE RECEPTOR / GLYCOPROTEIN / ANTIGEN:ANTIBODY COMPLEX / FAB FRAGMENT / ANTITUMOR / DRUG / Anti-oncogene / ATP-binding / Cell cycle / Disease mutation / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Secreted / Transferase / Transmembrane / Tyrosine-protein kinase / IMMUNE SYSTEM-TRANSFERASE COMPLEX
Function / homology
Function and homology information


positive regulation of protein kinase C activity / multivesicular body, internal vesicle lumen / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation / response to hydroxyisoflavone / diterpenoid metabolic process / Shc-EGFR complex / Inhibition of Signaling by Overexpressed EGFR / ovulation cycle / EGFR interacts with phospholipase C-gamma ...positive regulation of protein kinase C activity / multivesicular body, internal vesicle lumen / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation / response to hydroxyisoflavone / diterpenoid metabolic process / Shc-EGFR complex / Inhibition of Signaling by Overexpressed EGFR / ovulation cycle / EGFR interacts with phospholipase C-gamma / positive regulation of mucus secretion / epidermal growth factor binding / response to UV-A / tongue development / PLCG1 events in ERBB2 signaling / midgut development / ERBB2-EGFR signaling pathway / digestive tract morphogenesis / PTK6 promotes HIF1A stabilization / hydrogen peroxide metabolic process / morphogenesis of an epithelial fold / ERBB2 Activates PTK6 Signaling / Signaling by EGFR / transmembrane receptor protein tyrosine kinase activator activity / intracellular vesicle / response to cobalamin / eyelid development in camera-type eye / negative regulation of epidermal growth factor receptor signaling pathway / Signaling by ERBB4 / protein insertion into membrane / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / immunoglobulin complex / protein tyrosine kinase activator activity / Respiratory syncytial virus (RSV) attachment and entry / PI3K events in ERBB2 signaling / positive regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of mitotic cell cycle / MAP kinase kinase kinase activity / hair follicle development / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / positive regulation of G1/S transition of mitotic cell cycle / embryonic placenta development / GAB1 signalosome / positive regulation of bone resorption / regulation of peptidyl-tyrosine phosphorylation / positive regulation of phosphorylation / salivary gland morphogenesis / peptidyl-tyrosine autophosphorylation / positive regulation of glial cell proliferation / positive regulation of vasoconstriction / GRB2 events in EGFR signaling / Signaling by ERBB2 / transmembrane receptor protein tyrosine kinase activity / SHC1 events in EGFR signaling / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / EGFR Transactivation by Gastrin / GRB2 events in ERBB2 signaling / cellular response to epidermal growth factor stimulus / SHC1 events in ERBB2 signaling / positive regulation of DNA repair / cellular response to dexamethasone stimulus / ossification / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / basal plasma membrane / positive regulation of epithelial cell proliferation / positive regulation of superoxide anion generation / liver regeneration / epithelial cell proliferation / neurogenesis / positive regulation of DNA replication / Signal transduction by L1 / positive regulation of protein localization to plasma membrane / astrocyte activation / NOTCH3 Activation and Transmission of Signal to the Nucleus / epidermal growth factor receptor activity / positive regulation of smooth muscle cell proliferation / cellular response to amino acid stimulus / lung development / cellular response to estradiol stimulus / EGFR downregulation / clathrin-coated endocytic vesicle membrane / Signaling by ERBB2 TMD/JMD mutants / synaptic membrane / epidermal growth factor receptor signaling pathway / Constitutive Signaling by EGFRvIII / positive regulation of peptidyl-serine phosphorylation / Signaling by ERBB2 ECD mutants / receptor protein-tyrosine kinase / negative regulation of protein catabolic process / peptidyl-tyrosine phosphorylation / Signaling by ERBB2 KD Mutants / cell-cell adhesion / positive regulation of miRNA transcription / kinase binding / ruffle membrane / Downregulation of ERBB2 signaling / cellular response to mechanical stimulus / response to calcium ion
Similarity search - Function
24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-domain / : / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Alpha-Beta Horseshoe / Receptor L-domain / Furin-like cysteine-rich domain ...24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-domain / : / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Alpha-Beta Horseshoe / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / : / Growth factor receptor cysteine-rich domain superfamily / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Tyrosine-protein kinase, active site / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Epidermal growth factor receptor / IGH@ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.58 Å
AuthorsFerguson, K.M. / Li, S. / Kussie, P.
CitationJournal: Structure / Year: 2008
Title: Structural basis for EGF receptor inhibition by the therapeutic antibody IMC-11F8.
Authors: Li, S. / Kussie, P. / Ferguson, K.M.
History
DepositionOct 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_validate_close_contact / software
Item: _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 ..._pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: IMC-11F8 Fab Light chain
H: IMC-11F8 Fab Heavy chain
A: Epidermal growth factor receptor
D: IMC-11F8 Fab Light chain
C: IMC-11F8 Fab Heavy chain
B: Epidermal growth factor receptor
G: IMC-11F8 Fab Light chain
F: IMC-11F8 Fab Heavy chain
E: Epidermal growth factor receptor
K: IMC-11F8 Fab Light chain
J: IMC-11F8 Fab Heavy chain
I: Epidermal growth factor receptor
O: IMC-11F8 Fab Light chain
N: IMC-11F8 Fab Heavy chain
M: Epidermal growth factor receptor
R: IMC-11F8 Fab Light chain
Q: IMC-11F8 Fab Heavy chain
P: Epidermal growth factor receptor
U: IMC-11F8 Fab Light chain
T: IMC-11F8 Fab Heavy chain
S: Epidermal growth factor receptor
X: IMC-11F8 Fab Light chain
W: IMC-11F8 Fab Heavy chain
V: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)577,65164
Polymers563,55224
Non-polymers14,09940
Water18,6641036
1
L: IMC-11F8 Fab Light chain
H: IMC-11F8 Fab Heavy chain
A: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1568
Polymers70,4443
Non-polymers1,7125
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
MethodPISA
2
D: IMC-11F8 Fab Light chain
C: IMC-11F8 Fab Heavy chain
B: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8977
Polymers70,4443
Non-polymers1,4534
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6630 Å2
MethodPISA
3
G: IMC-11F8 Fab Light chain
F: IMC-11F8 Fab Heavy chain
E: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2529
Polymers70,4443
Non-polymers1,8086
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7070 Å2
MethodPISA
4
K: IMC-11F8 Fab Light chain
J: IMC-11F8 Fab Heavy chain
I: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5218
Polymers70,4443
Non-polymers2,0775
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
MethodPISA
5
O: IMC-11F8 Fab Light chain
N: IMC-11F8 Fab Heavy chain
M: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8458
Polymers70,4443
Non-polymers2,4015
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7470 Å2
MethodPISA
6
R: IMC-11F8 Fab Light chain
Q: IMC-11F8 Fab Heavy chain
P: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8977
Polymers70,4443
Non-polymers1,4534
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
MethodPISA
7
U: IMC-11F8 Fab Light chain
T: IMC-11F8 Fab Heavy chain
S: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9938
Polymers70,4443
Non-polymers1,5495
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6860 Å2
MethodPISA
8
X: IMC-11F8 Fab Light chain
W: IMC-11F8 Fab Heavy chain
V: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0909
Polymers70,4443
Non-polymers1,6456
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.373, 139.122, 175.325
Angle α, β, γ (deg.)90.000, 90.020, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 8 molecules ABEIMPSV

#3: Protein
Epidermal growth factor receptor / Receptor tyrosine-protein kinase ErbB-1


Mass: 23786.088 Da / Num. of mol.: 8 / Fragment: sequence database residues 335-538
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EGFR, ERBB1 / Production host: Mus musculus (house mouse) / Strain (production host): NS0
References: UniProt: P00533, receptor protein-tyrosine kinase

-
Antibody , 2 types, 16 molecules LDGKORUXHCFJNQTW

#1: Antibody
IMC-11F8 Fab Light chain


Mass: 23053.557 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EGFR / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
#2: Antibody
IMC-11F8 Fab Heavy chain


Mass: 23604.381 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse) / Strain (production host): NS0 / References: UniProt: Q6GMX6*PLUS

-
Sugars , 5 types, 32 molecules

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


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: 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.: 7
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
#7: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_d3-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(3+1)][a-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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 14
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

-
Non-polymers , 2 types, 1044 molecules

#9: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1036 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.34 Å3/Da / Density % sol: 63.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5
Details: 12 % PEG 3350, 0.25 M ammonium acetate, 50 mM sodium acetate, pH 5.0, vapor diffusion, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.57→50 Å / Num. all: 231454 / Num. obs: 231454 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 53 Å2 / Rmerge(I) obs: 0.097 / Χ2: 1.025 / Net I/σ(I): 9.7
Reflection shellResolution: 2.57→2.69 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 2.4 / Num. unique all: 22862 / Χ2: 0.991 / % possible all: 99

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
DMphasing
REFMACrefinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1yy9, 1ce1, and 1dn0

1yy9

1ce1

1dn0


Resolution: 2.58→43.07 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.843 / SU B: 23.221 / SU ML: 0.252 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.467 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.291 11664 5 %RANDOM
Rwork0.227 ---
all0.23 233995 --
obs0.23 231396 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.071 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å2-0.04 Å2
2--0.39 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.58→43.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37083 0 916 1036 39035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02238967
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.97953294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.70754952
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.39924.5381428
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.2155714
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.33415127
X-RAY DIFFRACTIONr_chiral_restr0.0930.26282
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0228878
X-RAY DIFFRACTIONr_nbd_refined0.2080.213579
X-RAY DIFFRACTIONr_nbtor_refined0.3030.225586
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.21357
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.25
X-RAY DIFFRACTIONr_mcbond_it0.4241.525370
X-RAY DIFFRACTIONr_mcangle_it0.757239910
X-RAY DIFFRACTIONr_scbond_it1.193315519
X-RAY DIFFRACTIONr_scangle_it1.9874.513384
LS refinement shellResolution: 2.58→2.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 773 -
Rwork0.32 13941 -
all-14714 -
obs-14714 85.95 %

+
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