SAXSdb — 9ut1

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

DNA replication helicase

Human alphaherpesvirus 1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 3 DNA 1	Ubiquitin-like protein SMT3,DNA primase × 1 （P10236,Q12306） Ubiquitin-like protein SMT3,DNA helicase/primase complex-associated protein × 1 （P10192,Q12306） synthetic DNA × 1 Amenamevir × 1 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HELI_HHV11
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 53–934； UniProt 1–882

Ubiquitin-like protein SMT3,DNA primase

Human alphaherpesvirus 1

UniProt P10236

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 3 DNA 1	DNA replication helicase × 1 （P10189） Ubiquitin-like protein SMT3,DNA helicase/primase complex-associated protein × 1 （P10192,Q12306） synthetic DNA × 1 Amenamevir × 1 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PRIM_HHV11
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 138–1195； UniProt 1–1058

Ubiquitin-like protein SMT3,DNA primase

Human alphaherpesvirus 1

UniProt Q12306

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 3 DNA 1	DNA replication helicase × 1 （P10189） synthetic DNA × 1 Amenamevir × 1 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SMT3_YEAST
Isoform	—
PDB entities	2, 3
Chains and sequence ranges	Author chain B； PDBConstruct 42–137； UniProt 3–98 Author chain C； PDBConstruct 42–137； UniProt 3–98

Ubiquitin-like protein SMT3,DNA helicase/primase complex-associated protein

Human alphaherpesvirus 1

UniProt P10192

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 3 DNA 1	DNA replication helicase × 1 （P10189） Ubiquitin-like protein SMT3,DNA primase × 1 （P10236,Q12306） synthetic DNA × 1 Amenamevir × 1 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HEPA_HHV11
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 138–887； UniProt 1–750

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	9ut1
Deposition date deposition_date	2025-05-02
Structure title title	The helicase-primase complex from HHV1 bound with ssDNA and amenamevir
Keywords keywords	Helicase, Primase, Inhibitor Complex, Herpesvirus, REPLICATION; REPLICATION
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.

9ut1__assembly_1__model_1

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

Download this curve (.dat)

9ut1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9ut1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	55.36 Å
Rg (electron density)	55.90 Å
Total Rg	55.76 Å
Atom count	18986
Residues	2443
Excluded volume	337380 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9ut1__assembly_1__model_1`	tetrameric （4）	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 (6)

Entity 1 Entity 1 polymer

Description description	DNA replication helicase
Molecular weight formula_weight	104354.2 kDa
EC 编号 ec_number	3.6.4.-
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	18986

MSYYGAWSHPQFEKGGGSGGGSGGSAWSHPQFEKGAHHHHHHGSLEVLFQGPMAAAGGERQLDGQKPGPPHLQQPGDRPAVPGRAEAFLNFTSMHGVQPILKRIRELSQQQLDGAQVPHLQWFRDVAALESPAGLPLREFPFAVYLITGNAGSGKSTCVQTINEVLDCVVTGATRIAAQNMYAKLSGAFLSRPINTIFHEFGFRGNHVQAQLGQYPYTLTSNPASLEDLQRRDLTYYWEVILDLTKRALAASGGEELRNEFRALAALERTLGLAEGALTRLAPATHGALPAFTRSNVIVIDEAGLLGRHLLTAVVYCWWMINALYHTPQYAARLRPVLVCVGSPTQTASLESTFEHQKLRCSVRQSENVLTYLICNRTLREYARLSYSWAIFINNKRCVEHEFGNLMKVLEYGLPITEEHMQFVDRFVVPENYITNPANLPGWTRLFSSHKEVSAYMAKLHAYLKVTREGEFVVFTLPVLTFVSVKEFDEYRRLTHQPGLTIEKWLTANASRITNYSQSQDQDAGHMRCEVHSKQQLVVARNDVTYVLNSQIAVTARLRKLVFGFSGTFRAFEAVLRDDSFVKTQGETSVEFAYRFLSRLIFSGLISFYNFLQRPGLDATQRTLAYARMGELTAEILSLRPKSSGVPTQASVMADAGAPGERAFDFKQLGPRDGGPDDFPDDDLDVIFAGLDEQQLDVFYCHYTPGEPETTAAVHTQFALLKRAFLGRFRILQELFGEAFEVAPFSTYVDNVIFRGCEMLTGSPRGGLMSVALQTDNYTLMGYTYARVFAFADELRRRHATANVAELLEEAPLPYVVLRDQHGFMSVVNTNISEFVESIDSTELAMAINADYGISSKLAMTITRSQGLSLDKVAICFTPGNLRLNSAYVAMSRTTSSEFLRMNLNPLRERHERDDVISEHILSALRDPNVVIVY

Source Source

Source organism organism	Human alphaherpesvirus 1
Common name common_name	Herpes simplex virus type 1
NCBI taxonomy ID ncbi_taxonomy_id	10298
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Ubiquitin-like protein SMT3,DNA primase
Molecular weight formula_weight	130399.0 kDa
EC 编号 ec_number	2.7.7.-
Mutation mutation	R64T/R71E
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSYYHHHHHHDYDIPTTENLYFQGITSLYKKAGFLQLGSLQDSEVNQEAKPEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLTFLYDGIEIQADQTPEDLDMEDNDIIEAHREQIGGMGQEDGNRGERRAAGTPVEVTALYATDGCVITSSIALLTNSLLGAEPVYIFSYDAYTHDGRADGPTEQDRFEESRALYQASGGLNGDSFRVTFCLLGTEVGGTHQARGRTRPMFVCRFERADDVAALQDALAHGTPLQPDHIAATLDAEATFALHANMILALTVAINNASPRTGRDAAAAQYDQGASLRSLVGRTSLGQRGLTTLYVHHEVRVLAAYRRAYYGSAQSPFWFLSKFGPDEKSLVLTTRYYLLQAQRLGGAGATYDLQAIKDICATYAIPHAPRPDTVSAASLTSFAAITRFCCTSQYARGAAAAGFPLYVERRIAADVRETSALEKFITHDRSCLRVSDREFITYIYLAHFECFSPPRLATHLRAVTTHDPNPAASTEQPSPLGREAVEQFFCHVRAQLNIGEYVKHNVTPRETVLDGDTAKAYLRARTYAPGALTPAPAYCGAVDSATKMMGRLADAEKLLVPRGWPAFAPASPGEDTAGGTPPPQTCGIVKRLLRLAATEQQGPTPPAIAALIRNAAVQTPLPVYRISMVPTGQAFAALAWDDWARITRDARLAEAVVSAEAAAHPDHGALGRRLTDRIRAQGPVMPPGGLDAGGQMYVNRNEIFNGALAITNIILDLDIALKEPVPFRRLHEALGHFRRGALAAVQLLFPAARVDPDAYPCYFFKSACRPGPASVGSGSGLGNDDDGDWFPCYDDAGDEEWAEDPGAMDTSHDPPDDEVAYFDLCHEVGPTAEPRETDSPVCSCTDKIGLRVCMPVPAPYVVHGSLTMRGVARVIQQAVLLDRDFVEAIGSYVKNFLLIDTGVYAHGHSLRLPYFAKIAPDGPACGRLLPVFVIPPACKDVPAFVAAHADPRRFHFHAPPTYLASPREIRVLHSLGGDYVSFFERKASRNALEHFGRRETLTEVLGRYNVQPDAGGTVEGFASELLGRIVACIETHFPEHAGEYQAVSVRRAVSKDDWVLLQLVPVRGTLQQSLSCLRFKHGRASRATARTFVALSVGANNRLCVSLCQQCFAAKCDSNRLHTLFTIDAGTPCSPSVPCSTSQPSS

Source Source

Source organism organism	Human alphaherpesvirus 1
Common name common_name	Herpes simplex virus type 1
NCBI taxonomy ID ncbi_taxonomy_id	10298
Host organism host_organism	Spodoptera frugiperda

Entity 3 Entity 3 polymer

Description description	Ubiquitin-like protein SMT3,DNA helicase/primase complex-associated protein
Molecular weight formula_weight	95846.4 kDa
Mutation mutation	R64T/R71E
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MSYYHHHHHHDYDIPTTENLYFQGITSLYKKAGFLQLGSLQDSEVNQEAKPEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLTFLYDGIEIQADQTPEDLDMEDNDIIEAHREQIGGMDTADIVWVEESVSAITLYAVWLPPRAREYFHALVYFVCRNAAGEGRARFAEVSVTATELRDFYGSADVSVQAVVAAARAATTPAASPLEPLENPTLWRALYACVLAALERQTGPVALFAPLRIGSDPRTGLVVKVERASWGPPAAPRAALLVAEANIDIDPMALAARVAEHPDARLAWARLAAIRDTPQCASAASLTVNITTGTALFAREYQTLAFPPIKKEGAFGDLVEVCEVGLRPRGHPQRVTARVLLPRDYDYFVSAGEKFSAPALVALFRQWHTTVHAAPGALAPVFAFLGPEFEVRGGPVPYFAVLGFPGWPTFTVPATAESARDLVRGAAAAYAALLGAWPAVGARVVLPPRAWPGVASAAAGCLLPAVREAVARWHPATKIIQLLDPPAAVGPVWTARFCFPGLRAQLLAALADLGGSGLADPHGRTGLARLDALVVAAPSEPWAGAVLERLVPDTCNACPALRQLLGGVMAAVCLQIEETASSVKFAVCGGDGGAFWGVFNVDPQDADAASGVIEDARRAIETAVGAVLRANAVRLRHPLCLALEGVYTHAVAWSQAGVWFWNSRDNTDHLGGFPLRGPAYTTAAGVVRDTLRRVLGLTTACVPEEDALTARGLMEDACDRLILDAFNKRLDAEYWSVRVSPFEASDPLPPTAFRGGALLDAEHYWRRVVRVCPGGGESVGVPVDLYPRPLVLPPVDCAHHLREILREIELVFTGVLAGVWGEGGKFVYPFDDKMSFLFA

Source Source

Source organism organism	Human alphaherpesvirus 1
Common name common_name	Herpes simplex virus type 1
NCBI taxonomy ID ncbi_taxonomy_id	10298
Host organism host_organism	Spodoptera frugiperda

Entity 4 Entity 4 polymer

Description description	synthetic DNA
Molecular weight formula_weight	2084.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

TTTTTTT

Entity 5 Entity 5 non-polymer

Description description	Amenamevir
Molecular weight formula_weight	482.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 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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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	triclinic

Resolution resolution	3.14 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	467000

The helicase-primase complex from HHV1 bound with ssDNA and amenamevir

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

DNA replication helicase

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin-like protein SMT3,DNA primase

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin-like protein SMT3,DNA primase

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin-like protein SMT3,DNA helicase/primase complex-associated protein

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

9ut1__assembly_1__model_1

9ut1__assembly_1__model_1 | I(q)

9ut1__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 (6)

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

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

7. Citations (1)

The helicase-primase complex from HHV1 bound with ssDNA and amenamevir

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

DNA replication helicase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ubiquitin-like protein SMT3,DNA primase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ubiquitin-like protein SMT3,DNA primase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ubiquitin-like protein SMT3,DNA helicase/primase complex-associated protein

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

9ut1__assembly_1__model_1

9ut1__assembly_1__model_1 | I(q)

9ut1__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 (6)

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

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

7. Citations (1)