SAXSdb — 7zn7

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

DNA damage-binding protein 1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	B27a × 1 （K7Y9Z1） Signal transducer and activator of transcription × 1 （Q5XI26） ZINC ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DDB1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–399； UniProt 1–396 Author chain A； PDBConstruct 406–840； UniProt 706–1140

B27a

Murid betaherpesvirus 8

UniProt K7Y9Z1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	DNA damage-binding protein 1 × 1 （Q16531） Signal transducer and activator of transcription × 1 （Q5XI26） ZINC ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	K7Y9Z1_RCMVE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–659； UniProt 1–656

Signal transducer and activator of transcription

Rattus norvegicus

UniProt Q5XI26

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	DNA damage-binding protein 1 × 1 （Q16531） B27a × 1 （K7Y9Z1） ZINC ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5XI26_RAT
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 4–845； UniProt 1–842

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	7zn7
Deposition date deposition_date	2022-04-20
Structure title title	Cryo-EM structure of RCMV-E E27 bound to human DDB1 (deltaBPB) and rat STAT2 CCD
Keywords keywords	;Interferon, ubiquitin-proteasome system, Cullin-RING ubiquitin ligases (CRL), DDB1, DCAFs, viral DCAF (vDCAF), cytomegalovirus, STAT2, IRF9, VIRUS ;; VIRUS
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.

7zn7__assembly_1__model_1

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

Download this curve (.dat)

7zn7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7zn7__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.75 Å
Rg (electron density)	36.19 Å
Total Rg	36.65 Å
Atom count	10497
Residues	1311
Excluded volume	187710 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7zn7__assembly_1__model_1`	trimeric （3）	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 (4)

Entity 1 Entity 1 polymer

Description description	DNA damage-binding protein 1
Molecular weight formula_weight	93671.5 kDa
Mutation mutation	delta396-705 GNGNSG
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	10497

GPGMSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIGNGNSGEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHETSFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	B27a
Molecular weight formula_weight	76341.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GPGMDLRDRQCESDRNEDNGETERQAIKERPNAMKIVFELIKDETADPFCRKFILDNLVQLKDIEQAARFGFAIEPGSEDYNRGVRSFIRLKEPYNHVELKMSYLKNARFATANGAYGIRGLTPAWDSAIWGLLREVEAVPYSNPFTFPTCERLEGILNRLEYRPEATDACRTLCRATVAVQYAISILYGYDRSASVPRYLRRLIDEYIDLQDRIRRLGIVPVLKISGKDMNIVQNVLPERVCAQIGIPFTYEACLLDEYYDCIESNIEQMYDLLCMCKECGMRRMERFERVRYNTIGERYPKKKRDRERFFEENYVIIHSHPDLGVLKLPKIRHLNPLQQLMMCRYLSKDLLYDTQFGPSNAFSRAQGVPLPFSAVQETDMNIAYALYLASNSYFMCFLLRCVRDVLRHEEEAFRKLILRLVNEAVEIIRDDVNSRVWAGADSPVFVCVDPRESGISAEERDLAIARSLEELTFSNELVEGSHFGGFCRDAARFLDLIDAFHFPKALREHRAREDLLLHTFKIEKMYDNRPLSAYYGDRLVPYHVLMGGHRRRDGAVVRTGGVNLTDNEIVRGHWRADDMMNARLRYFDSIDSIEMIRNVSIRQETLMFDLDRMYISRSELESLESDVESDNESEVLAGGACALPDRQSSSEVDSMCD

Source Source

Source organism organism	Murid betaherpesvirus 8
NCBI taxonomy ID ncbi_taxonomy_id	1261657
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Signal transducer and activator of transcription
Molecular weight formula_weight	97173.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

GPGMAQWEMLQNLDSPFLDQLHELYSQSLLPMDVRQHLAAWIEDQNWREAVLGSDHSKANMLYFNILDQLNQWDHYSLDSDYLLLQHNLRKFNRDIQMFPNGPTQLAEMIFNLLLEEKRILNQAQRAQEMQPRPAPEAAGESQQQLEIETRILDLQTAVEALVRSIRQLKDVQDVFSFRYTVLNHKKTSSLDPHQSQQRQLVQTTANELDRMRKEVLDISKALVGRLTTLVDLLLPKLDEWKAQQQKSCIGAPAPELQLDQLEQWLTAGAKVLFHLRQLLKQLKDMSLMLRYEGDMFGQGVDLQNAQVTELLQRLLQRSFVVETQPCMPQTLHRPLILKTGSKFTVRTRLLVRLQEGNESLKAEVSIDRNSELPGFRKFNILTSNQKSLTPEEGQRQGLIWDFGFLTLVEQRSVGAGKGSNKGPLPVTEELHIISAMVEYVYQGLKMKLQTDTLPVVIISNMNQLSIAWASILWFNMLSSTPKDQQFFCKVPKAPWSLLGPALSWQFSSYIGRGLDPEQLGMLRNKLFGKNCKTEDALLSWADFSKRESPPGKIPFWTWLDKILELVHDHLKDLWNDGRIMGFVSRSEERRLLKKMVSGTFLLRFSETSEGGITCSWVEHQDDDKVLIYSVQPYTKEVLQSLPLTEIIRHYQVLAEENAPENPLRFLYPRVPRDEAFGCYYQEKVNLEERRKYLKHRLIVISNRQADELQQPLELKQDPESLELDAELMSVMELARDLELQSMLQVGLDLGVEPKPDPTLSPAPQILLEPDPARALNQLLPEPDLPQDLQQLNTGEMEIFRNNINIDDVMPYGDPVLAGQSIIEEAYRSCPSHFDVDGPLIPSED

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Norway rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	7zn7A01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	7zn7A02
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	7zn7A03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	910 —

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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	—

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

Resolution resolution	3.78 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	389784

Cryo-EM structure of RCMV-E E27 bound to human DDB1 (deltaBPB) and rat STAT2 CCD

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

DNA damage-binding protein 1

State in the Current Structure

Other States of the Same Protein in the Database

B27a

State in the Current Structure

Other States of the Same Protein in the Database

Signal transducer and activator of transcription

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7zn7__assembly_1__model_1

7zn7__assembly_1__model_1 | I(q)

7zn7__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 (4)

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 non-polymer

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Cryo-EM structure of RCMV-E E27 bound to human DDB1 (deltaBPB) and rat STAT2 CCD

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

DNA damage-binding protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

B27a

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Signal transducer and activator of transcription

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

7zn7__assembly_1__model_1

7zn7__assembly_1__model_1 | I(q)

7zn7__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 (4)

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 non-polymer

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)