[English] 日本語
Yorodumi
- PDB-9iie: Cryogenic Temperature Crystal Structure of Fc Fragment of Human I... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9iie
TitleCryogenic Temperature Crystal Structure of Fc Fragment of Human IgG1 from Biosimilar VEGF-Trap
ComponentsImmunoglobulin gamma-1 heavy chain
KeywordsIMMUNE SYSTEM / N-glycans / immunoglobulin
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Immunoglobulin gamma-1 heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.14 Å
AuthorsDestan, E. / DeMirci, H.
Funding support Turkey, 1items
OrganizationGrant numberCountry
Other government Turkey
CitationJournal: Small Struct / Year: 2025
Title: Experimental and Computational Insights into the Structural Dynamics of the Fc Fragment of IgG1 Subtype from Biosimilar VEGF-Trap
Authors: Destan, E. / Turkut, E. / Aldeniz, A. / Kang, J. / Tosha, T. / Yabashi, M. / Yilmaz, B. / Timucin, C. / Matsuura, H. / Kawano, Y. / Cinkaya, I. / Demirci, H.
History
DepositionJun 20, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2May 21, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Immunoglobulin gamma-1 heavy chain
B: Immunoglobulin gamma-1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1554
Polymers47,2692
Non-polymers2,8862
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7490 Å2
ΔGint54 kcal/mol
Surface area21820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.920, 80.480, 137.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody Immunoglobulin gamma-1 heavy chain / Immunoglobulin gamma-1 heavy chain NIE


Mass: 23634.676 Da / Num. of mol.: 2 / Fragment: Fc Fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P0DOX5
#2: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1625.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DGlcpNAcb1-3DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/5,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1b_1-5]/1-1-2-3-1-3-1-4-5/a4-b1_a6-i1_b4-c1_c3-d1_c6-f1_d3-e1_f2-g1_g4-h1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(3+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][b-L-Fucp]{}}LINUCSPDB-CARE
#3: 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-ROHGlycam 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
[][D-1-deoxy-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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1M Bis-Tris pH 6.5, 25% w/v Polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1 Å
DetectorType: RIGAKU HyPix-Arc 150 / Detector: PIXEL / Date: Jun 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.14→137.08 Å / Num. obs: 9844 / % possible obs: 96.5 % / Redundancy: 3.6 % / CC1/2: 0.748 / CC star: 0.925 / Net I/σ(I): 2.26
Reflection shellResolution: 3.14→3.22 Å / Redundancy: 3.9 % / Num. unique obs: 683 / CC1/2: 0.155 / CC star: 0.518 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.14→23.84 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 29.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3086 805 10 %
Rwork0.2567 --
obs0.2621 8053 79.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.14→23.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3318 0 195 30 3543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033605
X-RAY DIFFRACTIONf_angle_d0.5034912
X-RAY DIFFRACTIONf_dihedral_angle_d14.4071396
X-RAY DIFFRACTIONf_chiral_restr0.043593
X-RAY DIFFRACTIONf_plane_restr0.004604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.14-3.340.41331180.34951063X-RAY DIFFRACTION72
3.34-3.590.37321210.29551096X-RAY DIFFRACTION74
3.59-3.950.30981270.2611139X-RAY DIFFRACTION76
3.95-4.520.29921310.23411176X-RAY DIFFRACTION77
4.52-5.680.25291450.21991316X-RAY DIFFRACTION86
5.68-23.840.26721630.23181458X-RAY DIFFRACTION90
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)
10.4366-0.2767-0.01731.7609-1.30991.335-0.26530.18170.2157-0.63430.1111-0.37770.24250.1562-0.02970.3129-0.2653-0.00570.2930.00120.2999-9.218212.923715.7762
25.4173-2.5911-1.30611.86162.17645.5144-0.00481.43050.0176-0.8907-0.3941-0.6647-1.04660.5640.22831.25550.06570.47751.19010.07910.6962-5.630112.9641-2.177
30.5774-1.21790.07923.3215-0.83860.61010.40880.5737-0.2934-0.8512-0.25910.5090.51430.084-0.19041.41420.4243-0.40580.88890.25781.2281-16.452316.3024.8118
43.85662.3937-1.01197.1037-3.72935.2490.0223-0.2208-0.1850.3438-0.2062-0.25680.05580.13210.17541.5242-0.35410.47281.21040.54821.33126.640516.54493.1534
52.11520.0361-0.54461.48410.18821.1974-0.0248-0.00010.3572-0.1196-0.0140.1054-0.19670.1380.01480.28660.07840.01550.19530.03110.1167-7.40698.468431.2116
61.4892-0.2169-1.37491.21440.54797.8547-0.11390.2221-0.3807-0.1249-0.08150.10230.0889-0.8636-0.01930.12650.01540.15770.19-0.04320.205613.0002-11.421718.3934
71.36510.5635-0.15611.85070.48160.1985-0.18490.2119-0.1665-0.4788-0.08490.0371-0.25020.03760.1930.3544-0.08960.17610.0876-0.12310.358416.1254-16.15689.4336
81.43820.79150.13920.87260.55060.5235-0.0584-0.11140.13730.20290.2237-0.3358-0.04280.0676-0.01010.25490.17730.08080.14610.01050.314425.3924-17.276911.7663
90.60961.1272-0.24672.6426-1.55442.25280.4712-0.2005-0.1212-0.32270.22930.6070.9618-0.7616-0.57950.3235-0.1243-0.07060.30090.00470.28644.7021-20.84992.2603
100.53090.31020.41931.8380.9181.3031-0.1986-0.19260.0787-0.2713-0.09710.17310.08750.1105-0.0968-0.01990.1010.12810.21090.0640.178820.4832-8.399516.2492
115.56610.6910.05180.561-1.10663.3420.0495-0.2280.17290.2623-0.0324-0.1414-0.2763-0.093-0.07040.18140.06640.19520.4683-0.07350.6138-4.9916-1.612247.5712
122.3324-0.46851.38372.9002-0.20763.063-0.3007-0.68220.0173-0.10350.2025-0.15470.3555-0.27010.06520.20790.00820.07210.22520.06230.29213.6122-8.641438.8277
134.14460.7883-0.19882.41661.03271.9514-0.0933-0.65340.09140.54670.00140.26480.0707-0.17490.10140.31120.19190.02550.1815-0.04930.12620.6823-2.780239.1929
145.2325-2.1703-2.67791.45112.43894.5733-0.5275-0.8039-0.73630.68620.5436-0.13160.98380.2187-0.06120.52530.1024-0.17710.27490.14250.62349.2908-9.921944.8588
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 223 through 249 )
2X-RAY DIFFRACTION2chain 'A' and (resid 250 through 264 )
3X-RAY DIFFRACTION3chain 'A' and (resid 265 through 275 )
4X-RAY DIFFRACTION4chain 'A' and (resid 276 through 286 )
5X-RAY DIFFRACTION5chain 'A' and (resid 287 through 429 )
6X-RAY DIFFRACTION6chain 'B' and (resid 222 through 236 )
7X-RAY DIFFRACTION7chain 'B' and (resid 237 through 264 )
8X-RAY DIFFRACTION8chain 'B' and (resid 265 through 275 )
9X-RAY DIFFRACTION9chain 'B' and (resid 276 through 286 )
10X-RAY DIFFRACTION10chain 'B' and (resid 287 through 331 )
11X-RAY DIFFRACTION11chain 'B' and (resid 332 through 346 )
12X-RAY DIFFRACTION12chain 'B' and (resid 347 through 378 )
13X-RAY DIFFRACTION13chain 'B' and (resid 379 through 403 )
14X-RAY DIFFRACTION14chain 'B' and (resid 404 through 428 )

+
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