[English] 日本語
Yorodumi
- PDB-4nqs: Knob-into-hole IgG Fc -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nqs
TitleKnob-into-hole IgG Fc
Components
  • (Ig gamma-1 chain C region) x 2
  • miniZ
KeywordsIMMUNE SYSTEM / 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 / Interleukin-4 and Interleukin-13 signaling / blood microparticle / 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)
Staphylococcus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsEigenbrot, C. / Ultsch, M.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Antiparallel Conformation of Knob and Hole Aglycosylated Half-Antibody Homodimers Is Mediated by a CH2-CH3 Hydrophobic Interaction.
Authors: Elliott, J.M. / Ultsch, M. / Lee, J. / Tong, R. / Takeda, K. / Spiess, C. / Eigenbrot, C. / Scheer, J.M.
History
DepositionNov 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
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
D: miniZ
E: miniZ
G: Ig gamma-1 chain C region
H: Ig gamma-1 chain C region
I: miniZ
J: miniZ


Theoretical massNumber of molelcules
Total (without water)113,1748
Polymers113,1748
Non-polymers00
Water21612
1
A: Ig gamma-1 chain C region
B: Ig gamma-1 chain C region
D: miniZ
E: miniZ


Theoretical massNumber of molelcules
Total (without water)56,5874
Polymers56,5874
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-21 kcal/mol
Surface area24740 Å2
MethodPISA
2
G: Ig gamma-1 chain C region
H: Ig gamma-1 chain C region
I: miniZ
J: miniZ


Theoretical massNumber of molelcules
Total (without water)56,5874
Polymers56,5874
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-20 kcal/mol
Surface area24800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.238, 66.083, 102.896
Angle α, β, γ (deg.)90.00, 95.18, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Ig gamma-1 chain C region / hole Fc T366S/L368A/Y407V


Mass: 24000.146 Da / Num. of mol.: 2 / Fragment: UNP residues 118-330 / Mutation: T366S/L368A/Y407V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01857
#2: Protein Ig gamma-1 chain C region / knob Fc T366W


Mass: 24205.400 Da / Num. of mol.: 2 / Fragment: UNP residues 118-330 / Mutation: T366W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01857
#3: Protein/peptide
miniZ


Mass: 4190.682 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Staphylococcus (bacteria)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsD356E and L358M (UNP D239E and L241M) ARE NATURAL VARIANTS.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG2000 MME, 10% 2-propanol, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 14, 2009
RadiationMonochromator: liquid nitrogen cooled dual crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.64→50 Å / Num. all: 30484 / Num. obs: 30472 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 56.12 Å2
Reflection shellHighest resolution: 2.64 Å

-
Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
BUSTER2.11.4refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1L6X

1l6x


Resolution: 2.64→46.5 Å / Cor.coef. Fo:Fc: 0.8939 / Cor.coef. Fo:Fc free: 0.8583 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 2.859 / SU Rfree Blow DPI: 0.345 / Stereochemistry target values: maxIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2657 961 3.15 %RANDOM
Rwork0.2286 ---
obs0.2298 30472 97.01 %-
all-30488 --
Displacement parametersBiso mean: 51.74 Å2
Baniso -1Baniso -2Baniso -3
1--3.6512 Å20 Å29.5724 Å2
2--4.9548 Å20 Å2
3----1.3036 Å2
Refine analyzeLuzzati coordinate error obs: 0.458 Å
Refinement stepCycle: LAST / Resolution: 2.64→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7820 0 0 12 7832
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0088034HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9910914HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2780SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes228HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1120HARMONIC5
X-RAY DIFFRACTIONt_it8034HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.3
X-RAY DIFFRACTIONt_other_torsion19.23
X-RAY DIFFRACTIONt_chiral_improper_torsion1009SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact8581SEMIHARMONIC4
LS refinement shellResolution: 2.64→2.73 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.3367 73 3.32 %
Rwork0.2649 2127 -
all0.2672 2200 -
obs--97.01 %
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)
1-0.06651.0060.46030.8921-0.4028.46780.008-0.5411-0.06770.3524-0.0847-0.09520.13560.03350.0767-0.2260.1448-0.04260.3040.0044-0.1621-49.28479.9714-33.8623
22.01970.55830.35941.80210.7714.8445-0.0372-0.29880.15510.1333-0.12540.3673-0.103-0.53350.1626-0.12660.01960.0007-0.0803-0.0255-0.0198-16.266227.7342-25.9996
32.74780.4382.15420.33230.05450.368-0.00720.2568-0.0601-0.2987-0.07290.4406-0.1375-0.37650.0802-0.17210.0768-0.06710.3040.0495-0.1124-21.59638.1727.349
43.69620.62650.87912.3710.79623.33180.047-0.33140.02420.3769-0.05280.22240.1431-0.49020.0059-0.06860.02790.05-0.08210.009-0.1228-16.5859-7.0029-26.7288
54.20840.03140.43991.67-0.06063.3141-0.1320.156-0.145-0.38420.15480.08490.30440.137-0.0228-0.0576-0.0094-0.031-0.10710.0109-0.1099-31.256310.3708-60.3546
64.7181-0.81651.64262.8425-1.91314.4524-0.06270.4730.2574-0.21150.0934-0.0559-0.0298-0.0628-0.0307-0.07310.00150.0093-0.1324-0.0513-0.0729-17.539919.6848-57.0409
73.6924-0.2095-0.45232.9092-1.16196.5870.00330.01870.31280.16330.1216-0.2507-0.17190.1152-0.1248-0.09860.0265-0.0483-0.1868-0.0062-0.10029.747110.3408-0.2074
82.1564-0.75970.75181.6512-0.05964.9587-0.0267-0.03430.11280.09460.1043-0.23140.28260.5427-0.0776-0.0773-0.019-0.0368-0.0706-0.0226-0.033711.7851.0419-14.1753
92.4464-1.8522.13130.964-1.14961.2070.03920.0808-0.2310.03150.0239-0.03530.0173-0.0586-0.0631-0.0561-0.0202-0.0255-0.10150.04680.1234-58.976511.3372-58.6537
106.5005-0.3703-1.30051.17330.26124.6516-0.0469-0.02690.0846-0.0420.0401-0.1297-0.04850.16150.0067-0.1242-0.01580.00370.0026-0.01160.01075.062622.7046-41.4123
110.05251.01961.66381.1838-0.82663.56890.0386-0.04370.0058-0.0690.02420.0141-0.27830.0133-0.06280.11960.04570.0136-0.1399-0.0066-0.0199-1.76559.424725.0583
123.98631.2055-2.10351.14121.05554.2276-0.0150.1529-0.0841-0.10020.0204-0.12970.15810.0469-0.0054-0.02660.01670.038-0.0429-0.0562-0.03565.6921-1.8923-40.9187
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|235 - A|341}A235 - 341
2X-RAY DIFFRACTION2{B|237 - B|341}B237 - 341
3X-RAY DIFFRACTION3{G|237 - G|341}G237 - 341
4X-RAY DIFFRACTION4{H|237 - H|341}H237 - 341
5X-RAY DIFFRACTION5{A|342 - A|444}A342 - 444
6X-RAY DIFFRACTION6{B|342 - B|443}B342 - 443
7X-RAY DIFFRACTION7{G|342 - G|444}G342 - 444
8X-RAY DIFFRACTION8{H|342 - H|443}H342 - 443
9X-RAY DIFFRACTION9{D|6 - D|39}D6 - 39
10X-RAY DIFFRACTION10{E|6 - E|39}E6 - 39
11X-RAY DIFFRACTION11{I|6 - I|39}I6 - 39
12X-RAY DIFFRACTION12{J|6 - J|39}J6 - 39

+
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