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- PDB-9mvx: Crystal structure of knob-in-hole immunoglobulin G1 Fc heterodime... -

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Basic information

Entry
Database: PDB / ID: 9mvx
TitleCrystal structure of knob-in-hole immunoglobulin G1 Fc heterodimer with P374A
Components
  • Isoform 1 of Immunoglobulin heavy constant gamma 1 HC1 (Hole)
  • Isoform 1 of Immunoglobulin heavy constant gamma 1 HC2 (Knob)
KeywordsIMMUNE SYSTEM / HUMAN FC FRAGMENT / IMMUNE RESPONSE / KNOB / HOLE / KNOB-IN-HOLE / KIH / ProAla / Proline-to-alanine / bispecific antibody / bsAb / bsIgG / Cis-peptide
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 / 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 / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Immunoglobulin heavy constant gamma 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsChoi, W.S. / Tilegenova, C. / Are, M. / Zwolak, A. / Shaffer, P. / Sharma, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat.Biotechnol. / Year: 2025
Title: Folding-mediated secretion of pure bispecific antibodies.
Authors: Tilegenova, C. / Liu, T. / Zhao, Q. / Are, M. / Zhao, Y. / Choi, W.S. / Bhaumik, A. / Steele, R. / Manieri, N.A. / Turegun, B. / Ni, A. / Cardoso, R.M.F. / Shaffer, P. / Clark, D. / Ernst, R. ...Authors: Tilegenova, C. / Liu, T. / Zhao, Q. / Are, M. / Zhao, Y. / Choi, W.S. / Bhaumik, A. / Steele, R. / Manieri, N.A. / Turegun, B. / Ni, A. / Cardoso, R.M.F. / Shaffer, P. / Clark, D. / Ernst, R. / Li, W. / Taylor, T. / Swaminathan, S.K. / Ramaraju, B. / Liaw, K. / Jacobs, S.A. / Sharma, S. / Cheung, W.C. / Zwolak, A.
History
DepositionJan 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 1 of Immunoglobulin heavy constant gamma 1 HC1 (Hole)
B: Isoform 1 of Immunoglobulin heavy constant gamma 1 HC2 (Knob)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9544
Polymers50,1742
Non-polymers2,7812
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6890 Å2
ΔGint47 kcal/mol
Surface area21360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.763, 81.014, 136.076
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Isoform 1 of Immunoglobulin heavy constant gamma 1 HC1 (Hole) / 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: 24985.240 Da / Num. of mol.: 1 / Mutation: I253D, T366S, L368A, P374A, Y407V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P01857
#2: Protein Isoform 1 of Immunoglobulin heavy constant gamma 1 HC2 (Knob) / 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: 25188.564 Da / Num. of mol.: 1 / Mutation: T366W, P374A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P01857
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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: 1317.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-1-3-1/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]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: 1463.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-1-3-1-4/a4-b1_a6-h1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O
Compound detailsThe two Fc chains switch positions in different asymmetric units, such that the HC1 (Hole) Fc ...The two Fc chains switch positions in different asymmetric units, such that the HC1 (Hole) Fc fragment is where chain A is located in a fraction of the asymmetric units, and it is where chain B is located in the remainder of the asymmetric units. Therefore, chain A and chain B were each modeled as 50% HC1 (Hole) and 50% HC2 (Knob).
Has ligand of interestN
Has protein modificationY

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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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 5% MPD, 0.1 M HEPES pH 7.5, 10% PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 25, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.836→69.611 Å / Num. obs: 45521 / % possible obs: 93 % / Redundancy: 6.2 % / Biso Wilson estimate: 40.09 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.033 / Rrim(I) all: 0.083 / Net I/σ(I): 9.8
Reflection shellResolution: 1.836→1.867 Å / Redundancy: 6.2 % / Rmerge(I) obs: 2.43 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2374 / CC1/2: 0.458 / Rpim(I) all: 1.053 / Rrim(I) all: 2.653 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→42.4 Å / SU ML: 0.2919 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.1259
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2547 2201 4.95 %
Rwork0.2109 42263 -
obs0.2131 44464 90.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.14 Å2
Refinement stepCycle: LAST / Resolution: 1.84→42.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3296 0 188 296 3780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00893610
X-RAY DIFFRACTIONf_angle_d1.00524950
X-RAY DIFFRACTIONf_chiral_restr0.0623599
X-RAY DIFFRACTIONf_plane_restr0.0085616
X-RAY DIFFRACTIONf_dihedral_angle_d6.6965578
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.880.43451150.44482189X-RAY DIFFRACTION77.6
1.88-1.920.4422630.40531511X-RAY DIFFRACTION51.78
1.92-1.970.3791250.34722374X-RAY DIFFRACTION83.44
1.97-2.020.36641600.3012859X-RAY DIFFRACTION99.31
2.02-2.080.33211270.27552341X-RAY DIFFRACTION81.67
2.08-2.150.25011610.25532832X-RAY DIFFRACTION99.7
2.15-2.220.28061350.25652882X-RAY DIFFRACTION99.7
2.22-2.310.30821410.24262478X-RAY DIFFRACTION86.09
2.31-2.420.29741370.22582886X-RAY DIFFRACTION99.77
2.42-2.550.29011560.22312880X-RAY DIFFRACTION99.84
2.55-2.70.27281450.2352646X-RAY DIFFRACTION91.51
2.7-2.910.35411520.24842930X-RAY DIFFRACTION99.94
2.91-3.210.29931360.24012931X-RAY DIFFRACTION100
3.21-3.640.28121400.20482590X-RAY DIFFRACTION92.83
3.68-4.620.18771540.1692804X-RAY DIFFRACTION95.82
4.62-42.40.20391540.17513130X-RAY DIFFRACTION99.94
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)
11.83569345614-0.359157783528-0.01467214630711.287833783971.665948665922.31770570142-0.345315453455-0.1423092775260.274578786344-1.03578200377-0.3893589242-0.5002993132430.2350329435860.175218254379-0.7723136874251.02751872822-0.07778410075450.2380911304560.3161359258710.2293948408470.423926098314-32.3469.98114.904
21.066265553960.3255289480980.01770682800510.2326635581660.3569122962291.38311613182-0.4632671193680.05888005214220.655593722867-1.20196229681-0.120939801472-0.4518492355120.2110796388090.253047318577-0.951183700161.10744197843-0.09730293644480.2547751268080.3375057496790.1847128182350.574065521452-32.32815.31612.657
30.01049719409890.0454323299701-0.01268010328180.300833518179-0.1781809015250.08351145371660.1992902044080.3740603722430.227019083877-0.61137098759-0.130141549329-0.157682389452-0.1037385805810.1326298500570.1289119228232.049912887850.142237117651-0.2644363088480.6193876184050.276096709750.480746384875-39.52214.6963.056
41.49412747256-0.3876610901640.05250480476272.194497858940.1983322544621.25405734047-0.204890638456-0.3794807220480.221224249212-0.1884682547280.141665168348-0.0862200393465-0.0238752605734-0.0458908213904-0.0056861565810.3140147765640.0177189968159-0.01175348644990.300616230173-0.06099789026570.393126194524-31.5288.87930.131
50.1439904828690.1396013913280.1067635179650.7389118817330.09664528009950.430513496966-0.005549312589230.00900234989256-0.11103604049-0.208251278847-0.05519606471590.01839742617930.216496767812-0.0618925205836-4.337798176020.458291131101-0.0170717850575-0.008575446175750.372844276005-0.02872801531310.302829199037-9.566-16.33310.843
60.409076573312-0.09548622468440.1358036793110.341192177066-0.3749728850350.266567060518-0.0331030385377-0.12582797730.0889907177847-0.2289269990250.100384663421-0.151569535593-0.08934824905980.0865631410669-0.00022922326150.359612914706-0.0126259044668-0.01688551059860.31092220142-0.01666149324970.326181403093-6.831-7.30820.837
70.273847688608-0.2386038619770.2541091805730.529252553161-0.4615660920960.4225812057260.194935282031-0.7281728178410.1194317292720.5472808791960.2872544111360.343735596805-0.472826061913-0.717134692141-0.01094300704760.5345056717510.1733984312850.253909880540.8651407810750.1788608647130.643257452014-34.897-4.59445.961
80.725812159078-0.2552270672730.07813101931730.1665216166490.343882051510.717290749763-0.1506765863-0.319150267153-0.29888135290.03530416127370.2256080330490.1261132641910.0416381443373-0.0915501511680.004091824612910.3448462900110.08165784020820.01197664218510.4598945012760.08092264813460.409265693202-19.862-7.45240.396
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 238:250 )A238 - 250
2X-RAY DIFFRACTION2( CHAIN A AND RESID 251:270 )A251 - 270
3X-RAY DIFFRACTION3( CHAIN A AND RESID 271:289 )A271 - 289
4X-RAY DIFFRACTION4( CHAIN A AND RESID 290:444 )A290 - 444
5X-RAY DIFFRACTION5( CHAIN B AND RESID 237:301 )B237 - 301
6X-RAY DIFFRACTION6( CHAIN B AND RESID 302:354 )B302 - 354
7X-RAY DIFFRACTION7( CHAIN B AND RESID 355:366 )B355 - 366
8X-RAY DIFFRACTION8( CHAIN B AND RESID 367:443 )B367 - 443

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