6oge

Cryo-EM structure of Her2 extracellular domain-Trastuzumab Fab-Pertuzumab Fab complex

Method: ELECTRON MICROSCOPY

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Receptor tyrosine-protein kinase erbB-2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 5 其他Polymer 1	Pertuzumab FAB LIGHT CHAIN × 1 （P01834） Pertuzumab FAB HEAVY CHAIN × 1 （P0DOX5） Trastuzumab FAB LIGHT CHAIN × 1 （P01834） Trastuzumab FAB HEAVY CHAIN × 1 （Q6GMX6） ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ERBB2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–622； UniProt 23–644

Pertuzumab FAB LIGHT CHAIN

Homo sapiens

UniProt P01834

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 5 其他Polymer 1	Receptor tyrosine-protein kinase erbB-2 × 1 （P04626） Pertuzumab FAB HEAVY CHAIN × 1 （P0DOX5） Trastuzumab FAB HEAVY CHAIN × 1 （Q6GMX6） ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IGKC_HUMAN
Isoform	—
PDB entities	2, 4
Chains and sequence ranges	Author chain B； PDBConstruct 108–214； UniProt 1–107 Author chain D； PDBConstruct 108–214； UniProt 1–107

Pertuzumab FAB HEAVY CHAIN

Homo sapiens

UniProt P0DOX5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 5 其他Polymer 1	Receptor tyrosine-protein kinase erbB-2 × 1 （P04626） Pertuzumab FAB LIGHT CHAIN × 1 （P01834） Trastuzumab FAB LIGHT CHAIN × 1 （P01834） Trastuzumab FAB HEAVY CHAIN × 1 （Q6GMX6） ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IGG1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 109–222； UniProt 109–222

Trastuzumab FAB HEAVY CHAIN

Homo sapiens

UniProt Q6GMX6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 5 其他Polymer 1	Receptor tyrosine-protein kinase erbB-2 × 1 （P04626） Pertuzumab FAB LIGHT CHAIN × 1 （P01834） Pertuzumab FAB HEAVY CHAIN × 1 （P0DOX5） Trastuzumab FAB LIGHT CHAIN × 1 （P01834） ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6GMX6_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 109–220； UniProt 124–235

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6oge
Deposition date deposition_date	2019-04-02
Structure title title	Cryo-EM structure of Her2 extracellular domain-Trastuzumab Fab-Pertuzumab Fab complex
Keywords keywords	Her2 extracellular domain, Trastuzumab, Pertuzumab, transferase-immune system complex; transferase/immune system
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6oge__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6oge__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6oge__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	45.88 Å
Rg (electron density)	45.56 Å
Total Rg	45.81 Å
Atom count	11494
Residues	1489
Excluded volume	202920 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6oge__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Receptor tyrosine-protein kinase erbB-2
Molecular weight formula_weight	68536.8 kDa
EC 编号 ec_number	2.7.10.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	11494

TQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGSRCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCAAGCTGPKHSDCLACLHFNHSGICELHCPALVTYNTDTFESMPNPEGRYTFGASCVTACPYNYLSTDVGSCTLVCPLHNQEVTAEDGTQRCEKCSKPCARVCYGLGMEHLREVRAVTSANIQEFAGCKKIFGSLAFLPESFDGDPASNTAPLQPEQLQVFETLEEITGYLYISAWPDSLPDLSVFQNLQVIRGRILHNGAYSLTLQGLGISWLGLRSLRELGSGLALIHHNTHLCFVHTVPWDQLFRNPHQALLHTANRPEDECVGEGLACHQLCARGHCWGPGPTQCVNCSQFLRGQECVEECRVLQGLPREYVNARHCLPCHPECQPQNGSVTCFGPEADQCVACAHYKDPPFCVARCPSGVKPDLSYMPIWKFPDEEGACQPCPINCTHSCVDLDDKGCPA

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Pertuzumab FAB LIGHT CHAIN
Molecular weight formula_weight	23548.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DIQMTQSPSSLSASVGDRVTITCKASQDVSIGVAWYQQKPGKAPKLLIYSASYRYTGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYYIYPYTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Cricetulus griseus

Entity 3 Entity 3 polymer

Description description	Pertuzumab FAB HEAVY CHAIN
Molecular weight formula_weight	23674.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

EVQLVESGGGLVQPGGSLRLSCAASGFTFTDYTMDWVRQAPGKGLEWVADVNPNSGGSIYNQRFKGRFTLSVDRSKNTLYLQMNSLRAEDTAVYYCARNLGPSFYFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Cricetulus griseus

Entity 4 Entity 4 polymer

Description description	Trastuzumab FAB LIGHT CHAIN
Molecular weight formula_weight	23466.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Cricetulus griseus

Entity 5 Entity 5 polymer

Description description	Trastuzumab FAB HEAVY CHAIN
Molecular weight formula_weight	23425.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYIHWVRQAPGKGLEWVARIYPTNGYTRYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRWGGDGFYAMDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Cricetulus griseus

Entity 6 Entity 6 branched

Description description	;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	748.7 kDa
Source method src_method	man
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	5

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	4.36 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	398409

Cryo-EM structure of Her2 extracellular domain-Trastuzumab Fab-Pertuzumab Fab complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

Receptor tyrosine-protein kinase erbB-2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Pertuzumab FAB LIGHT CHAIN

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Pertuzumab FAB HEAVY CHAIN

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Trastuzumab FAB HEAVY CHAIN

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6oge__assembly_1__model_1

6oge__assembly_1__model_1 | I(q)

6oge__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 branched

Entity 7 Entity 7 non-polymer

7. Citations (1)