[English] 日本語
Yorodumi
- PDB-3s7g: Aglycosylated human igg1 fc fragment -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3s7g
TitleAglycosylated human igg1 fc fragment
ComponentsIg gamma-1 chain C region
KeywordsIMMUNE SYSTEM / AGLYCOSYLATED / FC FRAGMENT / ANTIBODY / immunoglobulin
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: 3.13 Å
AuthorsBorrok, M.J. / Georgiou, G.
CitationJournal: To be Published
Title: Structural Analysis of an Aglycosylated Fc
Authors: Borrok, M.J. / Georgiou, G.
History
DepositionMay 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
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
C: Ig gamma-1 chain C region
D: Ig gamma-1 chain C region


Theoretical massNumber of molelcules
Total (without water)102,3244
Polymers102,3244
Non-polymers00
Water39622
1
A: Ig gamma-1 chain C region
B: Ig gamma-1 chain C region


Theoretical massNumber of molelcules
Total (without water)51,1622
Polymers51,1622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-11 kcal/mol
Surface area21500 Å2
MethodPISA
2
C: Ig gamma-1 chain C region
D: Ig gamma-1 chain C region


Theoretical massNumber of molelcules
Total (without water)51,1622
Polymers51,1622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-11 kcal/mol
Surface area21720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.689, 65.773, 77.811
Angle α, β, γ (deg.)98.18, 100.50, 116.92
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21B
31A
41D
12C
22B
32A
42D
13C
23A
33B
43D
14A
24C
15B
25D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112C238 - 294
2112B238 - 294
3112A238 - 294
4112D238 - 294
1122C343 - 443
2122B343 - 443
3122A343 - 443
4122D343 - 443
1132C300 - 337
2132A300 - 337
3132B300 - 337
4132D300 - 337
1143A295 - 299
2143C295 - 299
1153B295 - 299
2153D295 - 299

NCS ensembles :
ID
1
2
3
4
5

-
Components

#1: Protein
Ig gamma-1 chain C region


Mass: 25580.955 Da / Num. of mol.: 4 / Fragment: CH2 and CH3 regions, UNP RESIDUES 104-330
Source method: isolated from a genetically manipulated source
Details: FC PORTION OF IGG1 / Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1, IGHM / Plasmid: PTRC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH10B / References: UniProt: P01857
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.78 Å3/Da / Density % sol: 55.82 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10% PEG 1000, 20% PEG 6000, 0.1M MAGNESIUM CHLORIDE, 0.2M TRIS, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 2010
RadiationMonochromator: DOUBLE CRYSTAL SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.13→50 Å / Num. all: 19499 / Num. obs: 18883 / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Biso Wilson estimate: 87.2 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 12.6
Reflection shellResolution: 3.13→3.26 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 2.8 / % possible all: 97.1

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DNK (CH2 AND CH3 DOMAINS USED SEPARATELY)

3dnk


Resolution: 3.13→45 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.879 / SU B: 35.961 / SU ML: 0.623 / Cross valid method: THROUGHOUT / ESU R Free: 0.632 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.323 925 4.9 %RANDOM
Rwork0.259 ---
obs0.262 17958 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 89.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å21.08 Å23.87 Å2
2---1.77 Å20.74 Å2
3---3.8 Å2
Refinement stepCycle: LAST / Resolution: 3.13→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6640 0 0 22 6662
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0226832
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.9579313
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9385826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.33925304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.808151156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7581524
X-RAY DIFFRACTIONr_chiral_restr0.0950.21024
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0225184
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7151.54181
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.36626872
X-RAY DIFFRACTIONr_scbond_it1.54732651
X-RAY DIFFRACTIONr_scangle_it2.8484.52441
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11C228tight positional0.040.05
12B228tight positional0.050.05
13A228tight positional0.050.05
14D228tight positional0.040.05
21C400tight positional0.050.05
22B400tight positional0.050.05
23A400tight positional0.050.05
24D400tight positional0.050.05
31C152tight positional0.060.05
33B152tight positional0.050.05
32A152tight positional0.050.05
34D152tight positional0.050.05
41A20tight positional0.030.05
51B20tight positional0.040.05
11C232medium positional0.050.5
12B232medium positional0.050.5
13A232medium positional0.050.5
14D232medium positional0.050.5
21C404medium positional0.060.5
22B404medium positional0.060.5
23A404medium positional0.060.5
24D404medium positional0.060.5
31C152medium positional0.060.5
33B152medium positional0.060.5
32A152medium positional0.060.5
34D152medium positional0.060.5
42C22loose positional0.055
52D22loose positional0.055
11C228tight thermal0.10.5
12B228tight thermal0.10.5
13A228tight thermal0.090.5
14D228tight thermal0.110.5
21C400tight thermal0.10.5
22B400tight thermal0.10.5
23A400tight thermal0.10.5
24D400tight thermal0.110.5
31C152tight thermal0.10.5
33B152tight thermal0.090.5
32A152tight thermal0.080.5
34D152tight thermal0.110.5
41A20tight thermal0.030.5
51B20tight thermal0.040.5
11C232medium thermal0.092
12B232medium thermal0.092
13A232medium thermal0.092
14D232medium thermal0.092
21C404medium thermal0.112
22B404medium thermal0.12
23A404medium thermal0.12
24D404medium thermal0.112
31C152medium thermal0.112
33B152medium thermal0.12
32A152medium thermal0.12
34D152medium thermal0.122
42C22loose thermal0.0510
52D22loose thermal0.0510
LS refinement shellResolution: 3.13→3.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 51 -
Rwork0.351 1091 -
obs--80.65 %

+
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