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- PDB-9hiz: Complex of the Nanofitin Sac7d-C3(C24A) with a human IgG1 Fc fragment -

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Basic information

Entry
Database: PDB / ID: 9hiz
TitleComplex of the Nanofitin Sac7d-C3(C24A) with a human IgG1 Fc fragment
Components
  • DNA-binding protein 7d
  • Immunoglobulin heavy constant gamma 1
KeywordsPROTEIN BINDING / NANOFITIN / FC FRAGMENT / IGG1
Function / homology
Function and homology information


Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / complement activation, classical pathway ...Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / complement activation, classical pathway / Role of phospholipids in phagocytosis / antigen binding / RNA endonuclease activity / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / blood microparticle / adaptive immune response / DNA binding / extracellular space / extracellular exosome / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
DNA-binding 7kDa protein / 7kD DNA-binding domain / Chromo-like domain superfamily / : / 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. ...DNA-binding 7kDa protein / 7kD DNA-binding domain / Chromo-like domain superfamily / : / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Immunoglobulin heavy constant gamma 1 / DNA-binding protein 7d
Similarity search - Component
Biological speciesHomo sapiens (human)
Sulfolobus acidocaldarius DSM 639 (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsEichinger, A. / Skerra, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chembiochem / Year: 2025
Title: Engineering and Structural Elucidation of a Sac7d-Derived IgG Fc-Specific Affitin and Its Application for the Light-Controlled Affinity Purification of Antibodies.
Authors: Veitl, F. / Eichinger, A. / Mayrhofer, P. / Anneser, M.R. / Testanera, M. / Rauscher, K. / Lenz, M. / Skerra, A.
History
DepositionNov 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Immunoglobulin heavy constant gamma 1
B: Immunoglobulin heavy constant gamma 1
R: DNA-binding protein 7d
S: DNA-binding protein 7d
C: Immunoglobulin heavy constant gamma 1
D: Immunoglobulin heavy constant gamma 1
T: DNA-binding protein 7d
U: DNA-binding protein 7d


Theoretical massNumber of molelcules
Total (without water)130,6768
Polymers130,6768
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, The assembly contains two Fc-fragments (four heavy chains) and four nanofitin molecules
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12430 Å2
ΔGint-50 kcal/mol
Surface area54740 Å2
Unit cell
Length a, b, c (Å)68.270, 136.840, 69.760
Angle α, β, γ (deg.)90.00, 90.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Immunoglobulin heavy constant gamma 1 / Ig gamma-1 chain C region / Ig gamma-1 chain C region EU / Ig gamma-1 chain C region KOL / Ig gamma- ...Ig gamma-1 chain C region / Ig gamma-1 chain C region EU / Ig gamma-1 chain C region KOL / Ig gamma-1 chain C region NIE


Mass: 24780.988 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: N-terminal residues 228 - 235 of the sequence represent the methionine from the start codon followed by the affinity tag (His6-tag).
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Production host: Escherichia coli B (bacteria) / Strain (production host): Origami B / References: UniProt: P01857
#2: Protein
DNA-binding protein 7d / 7 kDa DNA-binding protein d / Sac7d


Mass: 7887.911 Da / Num. of mol.: 4
Mutation: K7L,Y8L,K9N,K21R,K22D,W24A,V26Q,M29N,S31K,T33L,D35N,T40Y,R42A,A44N,S46D
Source method: isolated from a genetically manipulated source
Details: The N-terminal residues DAEF were attached to the sequence for cloning purposes. We have named the mutation at position 24 "C24A" because it is based on the previously published Sac7d-C3 ...Details: The N-terminal residues DAEF were attached to the sequence for cloning purposes. We have named the mutation at position 24 "C24A" because it is based on the previously published Sac7d-C3 variant. Since we used here the wild-type sequence of Sac7d in UniProt for reference, this mutation is designated as W24A.
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: Saci_0064 / Production host: Escherichia coli B (bacteria) / Strain (production host): NEB Express / References: UniProt: P13123
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 24 % (w/v) PEG8000, 0.1 M Tris/HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 25, 2024
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.9→136.8 Å / Num. obs: 27577 / % possible obs: 97 % / Redundancy: 3.1 % / CC1/2: 0.994 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.119 / Net I/σ(I): 7.74
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.9-30.74827080.6760.9021
3-3.10.59723400.7850.7231
3.1-3.20.40120850.8650.4871
3.2-3.30.28117810.9250.3451
3.3-3.40.22816260.9550.2761
3.4-3.50.21114610.9690.2531
3.5-40.14251510.9810.1711
4-50.07350960.9930.0881
5-60.06422560.9940.0761
6-7.50.06315130.9930.0751
7.5-100.058930.9930.0611
10-150.0544710.9930.0631
15-200.051120.9930.061
20-300.055580.9930.0671
30-136.80.068260.9930.0851

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSJun 30, 2023data scaling
XDSJun 30, 2023data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→69.76 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.908 / SU B: 31.514 / SU ML: 0.454 / Cross valid method: THROUGHOUT / ESU R Free: 0.485 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27928 1379 5 %RANDOM
Rwork0.22729 ---
obs0.22991 26198 97.02 %-
Solvent computationIon probe radii: 1.2 Å / Shrinkage radii: 1.2 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 87.216 Å2
Baniso -1Baniso -2Baniso -3
1--5.23 Å20 Å2-0.99 Å2
2---1.91 Å2-0 Å2
3---7.15 Å2
Refinement stepCycle: 1 / Resolution: 2.9→69.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8892 0 0 0 8892
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0129096
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168572
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.85712324
X-RAY DIFFRACTIONr_angle_other_deg0.4811.78719900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.27551104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.02540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.34101624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0610.21340
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210540
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021956
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_it3.8627.4344440
X-RAY DIFFRACTIONr_mcbond_other3.8627.4344440
X-RAY DIFFRACTIONr_mcangle_it6.45913.3395536
X-RAY DIFFRACTIONr_mcangle_other6.45913.3395537
X-RAY DIFFRACTIONr_scbond_it3.4347.6794656
X-RAY DIFFRACTIONr_scbond_other3.4347.684657
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.89713.9996789
X-RAY DIFFRACTIONr_long_range_B_refined11.2669335491
X-RAY DIFFRACTIONr_long_range_B_other11.2669335492
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.449 104 -
Rwork0.392 1976 -
obs--98.91 %
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)
10.64080.60550.03450.83820.49522.9114-0.1991-0.11020.4848-0.0109-0.16710.46740.29760.73130.36610.14720.0158-0.12620.34160.04750.422730.43216.11118.231
22.68340.7283-0.13530.71740.29690.2213-0.12340.80280.56730.36170.17440.12770.2603-0.0602-0.05110.3133-0.0309-0.05040.36380.15220.124418.527-4.2796.75
31.7251-0.4034-1.17677.0872-4.401812.35190.0682-0.00790.2168-0.181-0.39120.1248-1.25420.45450.32290.7286-0.1022-0.11550.6957-0.02360.91728.79538.99628.632
48.34240.54641.27459.30030.7655.97950.15270.4129-0.4359-0.43460.0968-0.30420.1049-0.0163-0.24950.1672-0.01370.0420.428-0.0790.20788.865-27.4578.445
52.57510.2648-0.64524.58641.29541.17350.1226-0.8149-0.39370.78130.0085-0.20750.12670.198-0.13110.25380.0224-0.0490.57810.120.323552.691-20.90628.109
62.5277-1.0165-0.24314.1737-0.23243.3747-0.0838-0.2109-0.35950.1428-0.1264-0.2040.11310.82140.21010.11130.00570.02360.5220.06470.33264.494-41.25716.655
79.2567-0.5193-1.42346.8240.1684.76280.3596-0.3440.51310.4006-0.0917-0.43-0.2857-0.239-0.26790.1515-0.00190.01340.437-0.05150.215843.0512.45526.289
83.3481-1.27954.015110.6032-0.43177.23030.19320.0898-0.48210.3449-0.43070.1181.16730.56070.23750.73670.14190.15360.64870.02480.73263.01-63.9166.055
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A236 - 444
2X-RAY DIFFRACTION2B236 - 444
3X-RAY DIFFRACTION3C2 - 65
4X-RAY DIFFRACTION4D2 - 65
5X-RAY DIFFRACTION5E236 - 444
6X-RAY DIFFRACTION6F236 - 444
7X-RAY DIFFRACTION7G2 - 65
8X-RAY DIFFRACTION8H2 - 65

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