[English] 日本語
Yorodumi
- PDB-5k65: Crystal structure of VEGF binding IgG1-Fc (Fcab CT6) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5k65
TitleCrystal structure of VEGF binding IgG1-Fc (Fcab CT6)
ComponentsIg gamma-1 chain C region
KeywordsIMMUNE SYSTEM / antibody engineering / immunoglobulin G1 / Fc fragment / glycosylations / CH3 domain / Fcab / VEGF / vascular endothelial growth factor
Function / homology
Function and homology information


complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis ...complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis / complement activation, classical pathway / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / blood microparticle / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
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 ...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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin heavy constant gamma 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHumm, A. / Lobner, E. / Kitzmuller, M. / Mlynek, G. / Obinger, C. / Djinovic-Carugo, K.
Funding support Austria, 2items
OrganizationGrant numberCountry
Organization Christian Doppler Research AssociationChristian Doppler Laboratory for Antibody Engineering Austria
Austrian Science FundFWF W1224 (Doctoral Program on Biomolecular Technology of Proteins, BioTop) Austria
CitationJournal: MAbs / Year: 2017
Title: Two-faced Fcab prevents polymerization with VEGF and reveals thermodynamics and the 2.15 angstrom crystal structure of the complex.
Authors: Lobner, E. / Humm, A.S. / Mlynek, G. / Kubinger, K. / Kitzmuller, M. / Traxlmayr, M.W. / Djinovic-Carugo, K. / Obinger, C.
History
DepositionMay 24, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 11, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.occupancy / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_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_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ig gamma-1 chain C region
B: Ig gamma-1 chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1884
Polymers52,0172
Non-polymers2,1712
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint33 kcal/mol
Surface area22740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.490, 72.000, 168.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11B-632-

HOH

-
Components

#1: Protein Ig gamma-1 chain C region


Mass: 26008.578 Da / Num. of mol.: 2
Mutation: T359R, K360F, N361Y, E388D, N389I, 389aF, 389bP, 389cN, 389dG, 389eL, D413P, K414Y, S415P, R416S, Q418L, Q419M, N421T, V422R, S440H. S442E, L443Y, S444Q, P445W, G446P, K447T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Cell line (production host): HEK293-6E / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: P01857
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1260.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-1-4/a4-b1_a6-g1_b4-c1_c3-d1_c6-e1_e2-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Morpheus_C6 0.03M of each NPS: (sodium nitrate, disodium hydrogen phosphate, ammonium sulfate). 0.1M MOPS/HEPES-Na pH 7.5 10% w/v PEG 8000, 20% v/v ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 5, 2015 / Details: CRL
RadiationMonochromator: C(110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.5→48.028 Å / Num. obs: 25171 / % possible obs: 99 % / Redundancy: 4.4 % / Biso Wilson estimate: 64.62 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1254 / Net I/σ(I): 7.69
Reflection shellResolution: 2.5→2.589 Å / Redundancy: 4.7 % / Rmerge(I) obs: 1.871 / Mean I/σ(I) obs: 0.74 / % possible all: 100

-
Processing

Software
NameVersionClassification
EDNAdata collection
XDSv.Oct-2015data reduction
XDSv.Oct-2015data scaling
PHENIX1.10-2247phasing
PHENIX1.10-2247refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K64

5k64


Resolution: 2.5→48.028 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.2 / Phase error: 27.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2463 3709 7.97 %
Rwork0.221 --
obs0.223 46529 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→48.028 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3469 0 146 81 3696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033743
X-RAY DIFFRACTIONf_angle_d0.6335130
X-RAY DIFFRACTIONf_dihedral_angle_d9.4462253
X-RAY DIFFRACTIONf_chiral_restr0.045584
X-RAY DIFFRACTIONf_plane_restr0.003632
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.53290.3481390.37391655X-RAY DIFFRACTION99
2.5329-2.56760.45271480.36041664X-RAY DIFFRACTION99
2.5676-2.60430.32681370.35261645X-RAY DIFFRACTION99
2.6043-2.64320.33631460.36541695X-RAY DIFFRACTION98
2.6432-2.68450.38591350.3331619X-RAY DIFFRACTION98
2.6845-2.72850.34841460.34611675X-RAY DIFFRACTION98
2.7285-2.77550.37431430.33641665X-RAY DIFFRACTION99
2.7755-2.8260.36561440.33521671X-RAY DIFFRACTION99
2.826-2.88030.32431450.32271650X-RAY DIFFRACTION98
2.8803-2.93910.34551420.32781628X-RAY DIFFRACTION98
2.9391-3.0030.35471390.32571643X-RAY DIFFRACTION97
3.003-3.07290.29941430.31181614X-RAY DIFFRACTION96
3.0729-3.14970.27841450.30521617X-RAY DIFFRACTION97
3.1497-3.23480.30171440.26791660X-RAY DIFFRACTION98
3.2348-3.330.25211470.24581647X-RAY DIFFRACTION98
3.33-3.43740.27511470.2391694X-RAY DIFFRACTION98
3.4374-3.56030.27911410.22861625X-RAY DIFFRACTION98
3.5603-3.70280.26881430.22051670X-RAY DIFFRACTION99
3.7028-3.87120.22321410.22341685X-RAY DIFFRACTION99
3.8712-4.07520.2121390.18971636X-RAY DIFFRACTION99
4.0752-4.33040.22591470.16691629X-RAY DIFFRACTION98
4.3304-4.66450.17331450.14661636X-RAY DIFFRACTION97
4.6645-5.13340.16091380.1471633X-RAY DIFFRACTION96
5.1334-5.87510.21891350.16121591X-RAY DIFFRACTION95
5.8751-7.39760.20311420.1971660X-RAY DIFFRACTION98
7.3976-48.03670.21551480.1931613X-RAY DIFFRACTION97
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)
11.257-0.8618-1.48165.0549-1.05892.7094-0.241-0.3144-0.12550.9662-0.14830.0301-0.24180.20360.00010.9962-0.10050.02640.76-0.00270.6584-24.6262-24.451546.5917
22.66580.59150.54973.59611.67643.1345-0.0485-0.06480.12160.078-0.30330.4813-0.3905-0.3424-00.52930.0218-0.02880.5359-0.03140.6112-32.463-20.816714.4172
33.6810.27850.21122.38831.09040.71730.0297-1.6088-0.48030.8947-0.0179-0.33170.0130.05960.00020.8946-0.0596-0.16991.34950.11891.02515.3933-32.86327.0691
42.7197-0.59280.38333.4101-0.30083.2834-0.04160.2210.0562-0.0804-0.0546-0.3502-0.52410.301600.5848-0.0815-0.02180.5663-0.02470.6071-16.857-18.99796.5434
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 236 through 340 )
2X-RAY DIFFRACTION2chain 'A' and (resid 341 through 445 )
3X-RAY DIFFRACTION3chain 'B' and (resid 239 through 340 )
4X-RAY DIFFRACTION4chain 'B' and (resid 341 through 445 )

+
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