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- PDB-9iut: Crystal structure of cancer-specific anti-HER2 antibody H2Mab-250... -

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Basic information

Entry
Database: PDB / ID: 9iut
TitleCrystal structure of cancer-specific anti-HER2 antibody H2Mab-250 in complex with epitope peptide
Components
  • H2Mab-250 VH(S112C)-SARAH
  • H2Mab-250 VL-SARAH(S37C)
  • H2Mab-250 epitope peptide
KeywordsIMMUNE SYSTEM / Fv-clasp / antibody / cancer-specific / HER2
Function / homology
Function and homology information


negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / RNA polymerase I core binding / immature T cell proliferation in thymus / semaphorin receptor complex / ErbB-3 class receptor binding / motor neuron axon guidance / Sema4D induced cell migration and growth-cone collapse ...negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / RNA polymerase I core binding / immature T cell proliferation in thymus / semaphorin receptor complex / ErbB-3 class receptor binding / motor neuron axon guidance / Sema4D induced cell migration and growth-cone collapse / regulation of microtubule-based process / PLCG1 events in ERBB2 signaling / ERBB2-EGFR signaling pathway / neurotransmitter receptor localization to postsynaptic specialization membrane / ERBB2 Activates PTK6 Signaling / enzyme-linked receptor protein signaling pathway / neuromuscular junction development / positive regulation of Rho protein signal transduction / ERBB2-ERBB3 signaling pathway / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / positive regulation of MAP kinase activity / positive regulation of transcription by RNA polymerase I / ERBB2 Regulates Cell Motility / semaphorin-plexin signaling pathway / oligodendrocyte differentiation / PI3K events in ERBB2 signaling / positive regulation of protein targeting to membrane / regulation of angiogenesis / regulation of ERK1 and ERK2 cascade / Schwann cell development / coreceptor activity / Signaling by ERBB2 / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / myelination / transmembrane receptor protein tyrosine kinase activity / positive regulation of cell adhesion / GRB2 events in ERBB2 signaling / Downregulation of ERBB2:ERBB3 signaling / SHC1 events in ERBB2 signaling / cell surface receptor protein tyrosine kinase signaling pathway / basal plasma membrane / peptidyl-tyrosine phosphorylation / cellular response to epidermal growth factor stimulus / Constitutive Signaling by Overexpressed ERBB2 / positive regulation of translation / positive regulation of epithelial cell proliferation / neuromuscular junction / phosphatidylinositol 3-kinase/protein kinase B signal transduction / wound healing / Signaling by ERBB2 TMD/JMD mutants / receptor protein-tyrosine kinase / Signaling by ERBB2 ECD mutants / receptor tyrosine kinase binding / Signaling by ERBB2 KD Mutants / cellular response to growth factor stimulus / ruffle membrane / Downregulation of ERBB2 signaling / epidermal growth factor receptor signaling pathway / neuron differentiation / Constitutive Signaling by Aberrant PI3K in Cancer / transmembrane signaling receptor activity / PIP3 activates AKT signaling / myelin sheath / heart development / presynaptic membrane / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / positive regulation of cell growth / protein tyrosine kinase activity / basolateral plasma membrane / early endosome / cell surface receptor signaling pathway / cell population proliferation / protein phosphorylation / receptor complex / endosome membrane / positive regulation of MAPK cascade / intracellular signal transduction / apical plasma membrane / protein heterodimerization activity / signaling receptor binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / plasma membrane / cytosol
Similarity search - Function
: / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain ...: / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / Growth factor receptor cysteine-rich domain superfamily / : / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Receptor tyrosine-protein kinase erbB-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsArimori, T. / Takagi, J.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21H02416 Japan
CitationJournal: Cell Stem Cell / Year: 2025
Title: Preferential tumor targeting of HER2 by iPSC-derived CAR T cells engineered to overcome multiple barriers to solid tumor efficacy.
Authors: Hosking, M.P. / Shirinbak, S. / Omilusik, K. / Chandra, S. / Kaneko, M.K. / Gentile, A. / Yamamoto, S. / Shrestha, B. / Grant, J. / Boyett, M. / Cardenas, D. / Keegan, H. / Ibitokou, S. / ...Authors: Hosking, M.P. / Shirinbak, S. / Omilusik, K. / Chandra, S. / Kaneko, M.K. / Gentile, A. / Yamamoto, S. / Shrestha, B. / Grant, J. / Boyett, M. / Cardenas, D. / Keegan, H. / Ibitokou, S. / Pavon, C. / Mizoguchi, T. / Ihara, T. / Nakayama, D. / Abujarour, R. / Lee, T.T. / Clarke, R. / Goodridge, J. / Peralta, E. / Maeda, T. / Takagi, J. / Arimori, T. / Kato, Y. / Valamehr, B.
History
DepositionJul 22, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2025Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 16, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H2Mab-250 VH(S112C)-SARAH
B: H2Mab-250 VL-SARAH(S37C)
C: H2Mab-250 epitope peptide
D: H2Mab-250 VH(S112C)-SARAH
E: H2Mab-250 VL-SARAH(S37C)
F: H2Mab-250 epitope peptide


Theoretical massNumber of molelcules
Total (without water)77,9626
Polymers77,9626
Non-polymers00
Water6,738374
1
A: H2Mab-250 VH(S112C)-SARAH
B: H2Mab-250 VL-SARAH(S37C)
C: H2Mab-250 epitope peptide


Theoretical massNumber of molelcules
Total (without water)38,9813
Polymers38,9813
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-48 kcal/mol
Surface area17010 Å2
MethodPISA
2
D: H2Mab-250 VH(S112C)-SARAH
E: H2Mab-250 VL-SARAH(S37C)
F: H2Mab-250 epitope peptide


Theoretical massNumber of molelcules
Total (without water)38,9813
Polymers38,9813
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-47 kcal/mol
Surface area16270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.545, 123.199, 96.083
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-227-

HOH

21E-247-

HOH

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Components

#1: Antibody H2Mab-250 VH(S112C)-SARAH


Mass: 18801.139 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The VH domain region (residues 1-113) of this chimeric protein is derived from Mus musculus, while the SARAH domain region (residues 114-164) is derived from Homo sapiens.
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody H2Mab-250 VL-SARAH(S37C)


Mass: 19145.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The VL domain region (residues 1-108) of this chimeric protein is derived from Mus musculus, while the SARAH domain region (residues 109-159) is derived from Homo sapiens.
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Protein/peptide H2Mab-250 epitope peptide / Metastatic lymph node gene 19 protein / MLN 19 / Proto-oncogene Neu / Proto-oncogene c-ErbB-2 / ...Metastatic lymph node gene 19 protein / MLN 19 / Proto-oncogene Neu / Proto-oncogene c-ErbB-2 / Tyrosine kinase-type cell surface receptor HER2 / p185erbB2


Mass: 1034.250 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Receptor tyrosine-protein kinase erbB-2 / Source: (synth.) Homo sapiens (human)
References: UniProt: P04626, receptor protein-tyrosine kinase
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / Source method: isolated from a natural source / Formula: H2O
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: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.2 M MgCl2, 0.1 M Bis-Tris pH 5.7, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.09→42.3 Å / Num. obs: 41195 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 32.02 Å2 / CC1/2: 0.997 / Rsym value: 0.124 / Net I/σ(I): 10.66
Reflection shellResolution: 2.09→2.22 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 2.08 / Num. unique obs: 6539 / CC1/2: 0.798 / Rsym value: 0.83 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→37.07 Å / SU ML: 0.224 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.7927
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2358 2059 5 %
Rwork0.2012 39129 -
obs0.203 41188 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.6 Å2
Refinement stepCycle: LAST / Resolution: 2.09→37.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5297 0 0 374 5671
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00225402
X-RAY DIFFRACTIONf_angle_d0.55397302
X-RAY DIFFRACTIONf_chiral_restr0.0387800
X-RAY DIFFRACTIONf_plane_restr0.004936
X-RAY DIFFRACTIONf_dihedral_angle_d15.5569729
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.140.31741330.28642528X-RAY DIFFRACTION98.12
2.14-2.190.2731360.26892588X-RAY DIFFRACTION100
2.19-2.250.28371360.25932586X-RAY DIFFRACTION100
2.25-2.320.26551360.25232570X-RAY DIFFRACTION100
2.32-2.390.30311360.24072584X-RAY DIFFRACTION100
2.39-2.480.27981370.24062610X-RAY DIFFRACTION100
2.48-2.580.31370.23852597X-RAY DIFFRACTION100
2.58-2.690.27921350.2432583X-RAY DIFFRACTION100
2.69-2.840.2941380.24812616X-RAY DIFFRACTION99.96
2.84-3.010.26891370.23082590X-RAY DIFFRACTION100
3.01-3.250.24291380.22542623X-RAY DIFFRACTION99.89
3.25-3.570.25591370.19132604X-RAY DIFFRACTION99.93
3.57-4.090.20851380.16662636X-RAY DIFFRACTION99.82
4.09-5.150.16151400.14012658X-RAY DIFFRACTION99.68
5.15-37.070.18671450.16952756X-RAY DIFFRACTION99.62
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)
11.33234757310.614621065425-0.585201126932.9348224128-1.135295208742.12897129251-0.0158578993411-0.002921813148850.003460251362380.0429211894331-0.0484956476604-0.0432759975128-0.0304529663375-0.1317292080440.005941797452640.210441449376-0.0150575154209-0.01424022691810.40213588684-0.04169404030980.21745313130117.42820988444.87633695703-36.051333262
21.263774024410.202342463545-0.7881586139242.01414019089-0.7260785381641.762797404170.0465464803376-0.06247653779870.195074608238-0.0696190026905-0.0677122745621-0.0263581966652-0.109090411307-0.1808053426310.02928839546130.2102494032390.0205535959349-0.0207991022820.374924884745-0.01389473144870.25518175744519.21289201618.89739590335-38.9066337828
32.22885426382-0.194712385084-1.670618337752.225668655880.6208453632465.880361877370.1634516811270.4070744796670.6880937944720.1316532961130.0438357438890.388272113047-1.05114772363-0.632672027812-0.405864507540.657487628551-0.00792236294551-0.002813055221870.3899789347560.05544986073570.50690783809435.954878979726.6309488279-63.4037267261
4-0.185625334681-1.843928954892.298590892314.73451449902-6.564080843115.336800972710.1147430916290.139341109085-0.07740775847-0.0709444696381-0.13154465872-0.01177836076830.05795867735880.4837247356820.122668577580.370622686363-0.04532980778050.02727749392710.4850337629570.02784576155310.32639355695746.75707893555.85443153521-46.2226348806
52.63453379070.2289024336510.4398797628881.920522683760.0639314101183.509018260580.0590445853842-0.304100936646-0.01468038982190.134193165536-0.0547692893484-0.128992282068-0.0261245560027-0.02654234646360.002410043571490.223024849742-0.0396210187994-0.0131127827740.393512959197-0.03192916955340.22667847857124.31715155164.29214937087-16.9177786386
60.3158476551910.08685469091680.4338768000120.47606691846-0.07118699854741.0894976414-0.0651821354051-0.06736932500520.058725590218-0.03459414787810.0519429483583-0.06294314922220.165723044645-0.2543149425570.01978626819110.2249273867890.007421883968430.02667404689210.3549191239380.03240716844340.26635016990338.08489601634.53534752629-40.9179056811
76.12493199019-0.09292388099770.399069395415.04053964662-1.898761536374.895813635460.39973166309-0.485394993085-0.1497879340830.4830082440750.04441076686060.39349341323-0.292143918218-0.468162515291-0.5311940604710.319667511494-0.09665139916340.05313812930940.562742740426-0.0792990539890.2776823508048.563511678962.88475064925-23.2310228798
83.09027439089-0.8166187795981.226239409441.77361510745-1.14526196811.3073376180.03757816718790.4479593684270.140527631894-0.294756754182-0.05912601285340.08690157336530.02092507849370.0172226974480.01666687768570.2928175380650.00567883311639-0.03204026074130.4568940941350.02156280117830.26612218015850.979262667220.2520790784-12.346448799
96.055189298921.484868501875.129611752153.314333925741.557687369036.607115044520.0646551358538-0.24606546341-0.2639634896290.0765772832705-0.2653608301630.5693180801210.746841688464-0.889220504719-0.04801115987040.374768363794-0.101639698215-0.01103390711120.5612233355940.01558202323570.46337037059130.288641521738.2834502888-36.1983836851
106.576653700452.498986085316.707751246771.75050387582.620064494357.73730254005-0.185947735070.2364880265540.152607176371-0.06538167023190.1155658041010.102386396817-0.148311844110.1861445368810.06452966161540.2069568938180.03704788649260.03458333990360.2854476534640.01131416093360.20669219752652.629485075748.6715235483-21.4393470057
111.883613559620.5600228133420.2799168322774.91610569211-0.7270316221082.67288696234-0.0396725030618-0.1282258241220.1125427463660.158893690012-0.0291503622064-0.0440450122099-0.0813741796559-0.1171910353480.06895623762130.2227734680070.02299983747980.00395733192880.3382862430760.01083564581140.22726028799755.364040579827.18290619057.69535352966
123.642575464930.551905550073.099981904660.3294129687050.2745751917714.174212551720.0942720350001-0.163367017141-0.09038474558690.1002192635570.03785531925860.003645297582630.1888817761710.0702823372435-0.08719269752670.2814189974050.03752677860650.01598103341810.3140612294360.03434253881640.27941483640155.728029201941.5829248213-13.8619904614
134.263481836350.378205275026-0.5672776839345.792163428081.822974907925.50286822274-0.225976344379-0.401539373509-0.8058222652490.2444894289810.1420747160930.04481639820740.978087610950.08058368629490.001276655440180.3643747058430.04494699094420.03731065992080.2340171404320.03077553152470.41400468071654.622492502810.41703147482.03144690301
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -1 through 60 )AA-1 - 601 - 63
22chain 'A' and (resid 61 through 117 )AA61 - 11764 - 122
33chain 'A' and (resid 118 through 124 )AA118 - 124123 - 129
44chain 'A' and (resid 125 through 162 )AA125 - 162130 - 167
55chain 'B' and (resid 0 through 101 )BB0 - 1011 - 107
66chain 'B' and (resid 102 through 164 )BB102 - 164108 - 164
77chain 'C' and (resid 611 through 618 )CC611 - 6181 - 8
88chain 'D' and (resid 0 through 117 )DD0 - 1171 - 121
99chain 'D' and (resid 118 through 124 )DD118 - 124122 - 128
1010chain 'D' and (resid 125 through 162 )DD125 - 162129 - 166
1111chain 'E' and (resid 1 through 101 )EE1 - 1011 - 106
1212chain 'E' and (resid 102 through 159 )EE102 - 159107 - 159
1313chain 'F' and (resid 611 through 618 )FF611 - 6181 - 8

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