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Basic information

Entry
Database: PDB / ID: 4ypg
TitleStructural Insights Into the Neutralization Properties of a Human Anti-Interferon Monoclonal Antibody
Components
  • Interferon alpha-2Interferon type I
  • Sifalimumab heavy chain
  • Sifalimumab light chain
KeywordsIMMUNE SYSTEM / therapeutic mAb / IFN-alpha2A
Function / homology
Function and homology information


type I interferon receptor binding / cell surface receptor signaling pathway via STAT / negative regulation of interleukin-5 production / negative regulation of interleukin-13 production / negative regulation of T cell differentiation / natural killer cell activation involved in immune response / positive regulation of peptidyl-serine phosphorylation of STAT protein / negative regulation of T-helper 2 cell cytokine production / T cell activation involved in immune response / negative regulation of viral entry into host cell ...type I interferon receptor binding / cell surface receptor signaling pathway via STAT / negative regulation of interleukin-5 production / negative regulation of interleukin-13 production / negative regulation of T cell differentiation / natural killer cell activation involved in immune response / positive regulation of peptidyl-serine phosphorylation of STAT protein / negative regulation of T-helper 2 cell cytokine production / T cell activation involved in immune response / negative regulation of viral entry into host cell / TRAF6 mediated IRF7 activation / response to exogenous dsRNA / type I interferon-mediated signaling pathway / B cell proliferation / humoral immune response / Regulation of IFNA/IFNB signaling / B cell differentiation / cytokine activity / cellular response to virus / cytokine-mediated signaling pathway / Interferon alpha/beta signaling / cell-cell signaling / Factors involved in megakaryocyte development and platelet production / collagen-containing extracellular matrix / defense response to virus / adaptive immune response / cell surface receptor signaling pathway / inflammatory response / negative regulation of gene expression / negative regulation of DNA-templated transcription / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / extracellular space / extracellular region
Similarity search - Function
Interferon alpha, beta and delta family signature. / Interferon alpha, beta and delta. / Interferon alpha/beta/delta / Interferon alpha/beta domain / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain ...Interferon alpha, beta and delta family signature. / Interferon alpha, beta and delta. / Interferon alpha/beta/delta / Interferon alpha/beta domain / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / 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 / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / Interferon alpha-2 / IGK@ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsOganesyan, V. / Dall'Acqua, W.F.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Insights into the Neutralization Properties of the Fully Human, Anti-interferon Monoclonal Antibody Sifalimumab.
Authors: Oganesyan, V. / Peng, L. / Woods, R.M. / Wu, H. / Dall'Acqua, W.F.
History
DepositionMar 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2Jun 24, 2015Group: Database references
Revision 2.0Feb 13, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / entity_src_gen / pdbx_nonpoly_scheme / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_struct_special_symmetry / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn / struct_keywords / 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 / _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_keywords.text / _struct_site_gen.auth_seq_id
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sifalimumab light chain
B: Sifalimumab heavy chain
C: Interferon alpha-2
D: Interferon alpha-2
H: Sifalimumab heavy chain
L: Sifalimumab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,14912
Polymers130,7976
Non-polymers3526
Water84747
1
A: Sifalimumab light chain
B: Sifalimumab heavy chain
C: Interferon alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5756
Polymers65,3983
Non-polymers1763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6200 Å2
ΔGint-48 kcal/mol
Surface area26320 Å2
MethodPISA
2
D: Interferon alpha-2
H: Sifalimumab heavy chain
L: Sifalimumab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5756
Polymers65,3983
Non-polymers1763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-53 kcal/mol
Surface area26460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.820, 153.260, 163.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-301-

NI

21H-301-

NI

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21L
12B
22H
13C
23D

NCS domain segments:

Refine code: 4

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLULYSLYSAA1 - 401 - 40
211GLUGLULYSLYSLF1 - 401 - 40
121PROPROGLUGLUAA41 - 10641 - 106
221PROPROGLUGLULF41 - 10641 - 106
131ILEILESERSERAA107 - 177107 - 177
231ILEILESERSERLF107 - 177107 - 177
141SERSERCYSCYSAA178 - 215178 - 215
241SERSERCYSCYSLF178 - 215178 - 215
112GLNGLNGLNGLNBB1 - 621 - 62
212GLNGLNGLNGLNHE1 - 621 - 62
122LYSLYSPROPROBB63 - 12963 - 129
222LYSLYSPROPROHE63 - 12963 - 129
132SERSERVALVALBB130 - 185130 - 185
232SERSERVALVALHE130 - 185130 - 185
142THRTHRCYSCYSBB186 - 219186 - 219
242THRTHRCYSCYSHE186 - 219186 - 219
113THRTHRGLNGLNCC-1 - 201 - 22
213THRTHRGLNGLNDD-1 - 201 - 22
123METMETGLUGLUCC21 - 5123 - 53
223METMETGLUGLUDD21 - 5123 - 53
133THRTHRGLUGLUCC52 - 11354 - 115
233THRTHRGLUGLUDD52 - 11354 - 115
143ASPASPLEULEUCC114 - 157116 - 159
243ASPASPLEULEUDD114 - 157116 - 159

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody Sifalimumab light chain


Mass: 23431.963 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: homo sapiens (human) / References: UniProt: Q6PJF2
#2: Antibody Sifalimumab heavy chain


Mass: 23216.990 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: homo sapiens (human)
#3: Protein Interferon alpha-2 / Interferon type I / IFN-alpha-2 / Interferon alpha-A / LeIF A


Mass: 18749.475 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFNA2, IFNA2A, IFNA2B, IFNA2C / Production host: Escherichia coli (E. coli) / References: UniProt: P01563
#4: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.01 M NiCl2, 0.1 M Tris HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3→21 Å / Num. obs: 34084 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 7.8
Reflection shellResolution: 3→3.1 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.7 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RH2

1rh2


Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.884 / SU B: 39.576 / SU ML: 0.337 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.443 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27166 1719 5.1 %RANDOM
Rwork0.20611 ---
obs0.20942 30594 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.985 Å2
Baniso -1Baniso -2Baniso -3
1--2.81 Å20 Å20 Å2
2--2.3 Å20 Å2
3---0.5 Å2
Refinement stepCycle: 1 / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9166 0 6 47 9219
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0229378
X-RAY DIFFRACTIONr_bond_other_d0.0020.026346
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.95712738
X-RAY DIFFRACTIONr_angle_other_deg0.8673.00315492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.48551182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02624.188382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.126151568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1861546
X-RAY DIFFRACTIONr_chiral_restr0.0730.21438
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210388
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021864
X-RAY DIFFRACTIONr_nbd_refined0.2260.22212
X-RAY DIFFRACTIONr_nbd_other0.1950.26685
X-RAY DIFFRACTIONr_nbtor_refined0.1910.24508
X-RAY DIFFRACTIONr_nbtor_other0.0890.25208
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2273
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0110.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0940.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.242
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1980.299
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3781.57562
X-RAY DIFFRACTIONr_mcbond_other0.0561.52391
X-RAY DIFFRACTIONr_mcangle_it0.47129576
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.71834143
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.1354.53162
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
1A2799medium positional0.290.5
2B2729medium positional0.310.5
3C2213medium positional0.520.5
1A2799medium thermal0.212
2B2729medium thermal0.222
3C2213medium thermal0.262
LS refinement shellResolution: 3→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 124 -
Rwork0.28 2313 -
obs--99.19 %

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