5zr1

Saccharomyces Cerevisiae Origin Recognition Complex Bound to a 72-bp Origin DNA containing ACS and B1 element

Method: ELECTRON MICROSCOPY

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

Origin recognition complex subunit 1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 6 DNA 2	Origin recognition complex subunit 2 × 1 （P32833） Origin recognition complex subunit 3 × 1 （P54790） Origin recognition complex subunit 4 × 1 （P54791） Origin recognition complex subunit 5 × 1 （P50874） Origin recognition complex subunit 6 × 1 （P38826） 72bp-oring DNA, ACS305, T-rich × 1 72bp-oring DNA, ACS305, A-rich × 1 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MAGNESIUM ION × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ORC1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–914； UniProt 1–914

Origin recognition complex subunit 2

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P32833

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 6 DNA 2	Origin recognition complex subunit 1 × 1 （P54784） Origin recognition complex subunit 3 × 1 （P54790） Origin recognition complex subunit 4 × 1 （P54791） Origin recognition complex subunit 5 × 1 （P50874） Origin recognition complex subunit 6 × 1 （P38826） 72bp-oring DNA, ACS305, T-rich × 1 72bp-oring DNA, ACS305, A-rich × 1 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MAGNESIUM ION × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ORC2_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–620； UniProt 1–620

Origin recognition complex subunit 3

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P54790

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 6 DNA 2	Origin recognition complex subunit 1 × 1 （P54784） Origin recognition complex subunit 2 × 1 （P32833） Origin recognition complex subunit 4 × 1 （P54791） Origin recognition complex subunit 5 × 1 （P50874） Origin recognition complex subunit 6 × 1 （P38826） 72bp-oring DNA, ACS305, T-rich × 1 72bp-oring DNA, ACS305, A-rich × 1 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MAGNESIUM ION × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ORC3_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–616； UniProt 1–616

Origin recognition complex subunit 4

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P54791

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 6 DNA 2	Origin recognition complex subunit 1 × 1 （P54784） Origin recognition complex subunit 2 × 1 （P32833） Origin recognition complex subunit 3 × 1 （P54790） Origin recognition complex subunit 5 × 1 （P50874） Origin recognition complex subunit 6 × 1 （P38826） 72bp-oring DNA, ACS305, T-rich × 1 72bp-oring DNA, ACS305, A-rich × 1 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MAGNESIUM ION × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ORC4_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–529； UniProt 1–529

Origin recognition complex subunit 5

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P50874

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 6 DNA 2	Origin recognition complex subunit 1 × 1 （P54784） Origin recognition complex subunit 2 × 1 （P32833） Origin recognition complex subunit 3 × 1 （P54790） Origin recognition complex subunit 4 × 1 （P54791） Origin recognition complex subunit 6 × 1 （P38826） 72bp-oring DNA, ACS305, T-rich × 1 72bp-oring DNA, ACS305, A-rich × 1 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MAGNESIUM ION × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ORC5_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–479； UniProt 1–479

Origin recognition complex subunit 6

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P38826

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 6 DNA 2	Origin recognition complex subunit 1 × 1 （P54784） Origin recognition complex subunit 2 × 1 （P32833） Origin recognition complex subunit 3 × 1 （P54790） Origin recognition complex subunit 4 × 1 （P54791） Origin recognition complex subunit 5 × 1 （P50874） 72bp-oring DNA, ACS305, T-rich × 1 72bp-oring DNA, ACS305, A-rich × 1 PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MAGNESIUM ION × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ORC6_YEAST
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain F； PDBConstruct 1–435； UniProt 1–435

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	5zr1
Deposition date deposition_date	2018-04-21
Structure title title	Saccharomyces Cerevisiae Origin Recognition Complex Bound to a 72-bp Origin DNA containing ACS and B1 element
Keywords keywords	Origin Recognition Complex, DNA replication initiation, 72-bp origin DNA, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
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.

5zr1__assembly_1__model_1

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

Download this curve (.dat)

5zr1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5zr1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	46.35 Å
Rg (electron density)	46.28 Å
Total Rg	46.46 Å
Atom count	22260
Residues	2591
Excluded volume	394440 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5zr1__assembly_1__model_1`	octameric （8）	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 (10)

Entity 1 Entity 1 polymer

Description description	Origin recognition complex subunit 1
Molecular weight formula_weight	104546.2 kDa
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	22260

MAKTLKDLQGWEIITTDEQGNIIDGGQKRLRRRGAKTEHYLKRSSDGIKLGRGDSVVMHNEAAGTYSVYMIQELRLNTLNNVVELWALTYLRWFEVNPLAHYRQFNPDANILNRPLNYYNKLFSETANKNELYLTAELAELQLFNFIRVANVMDGSKWEVLKGNVDPERDFTVRYICEPTGEKFVDINIEDVKAYIKKVEPREAQEYLKDLTLPSKKKEIKRGPQKKDKATQTAQISDAETRATDITDNEDGNEDESSDYESPSDIDVSEDMDSGEISADELEEEEDEEEDEDEEEKEARHTNSPRKRGRKIKLGKDDIDASVQPPPKKRGRKPKDPSKPRQMLLISSCRANNTPVIRKFTKKNVARAKKKYTPFSKRFKSIAAIPDLTSLPEFYGNSSELMASRFENKLKTTQKHQIVETIFSKVKKQLNSSYVKEEILKSANFQDYLPARENEFASIYLSAYSAIESDSATTIYVAGTPGVGKTLTVREVVKELLSSSAQREIPDFLYVEINGLKMVKPTDCYETLWNKVSGERLTWAASMESLEFYFKRVPKNKKKTIVVLLDELDAMVTKSQDIMYNFFNWTTYENAKLIVIAVANTMDLPERQLGNKITSRIGFTRIMFTGYTHEELKNIIDLRLKGLNDSFFYVDTKTGNAILIDAAGNDTTVKQTLPEDVRKVRLRMSADAIEIASRKVASVSGDARRALKVCKRAAEIAEKHYMAKHGYGYDGKTVIEDENEEQIYDDEDKDLIESNKAKDDNDDDDDNDGVQTVHITHVMKALNETLNSHVITFMTRLSFTAKLFIYALLNLMKKNGSQEQELGDIVDEIKLLIEVNGSNKFVMEIAKTLFQQGSDNISEQLRIISWDFVLNQLLDAGILFKQTMKNDRICCVKLNISVEEAKRAMNEDETLRNL

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Saccharomyces cerevisiae

Entity 2 Entity 2 polymer

Description description	Origin recognition complex subunit 2
Molecular weight formula_weight	71342.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MLNGEDFVEHNDILSSPAKSRNVTPKRVDPHGERQLRRIHSSKKNLLERISLVGNERKNTSPDPALKPKTPSKAPRKRGRPRKIQEELTDRIKKDEKDTISSKKKRKLDKDTSGNVNEESKTSNNKQVMEKTGIKEKREREKIQVATTTYEDNVTPQTDDNFVSNSPEPPEPATPSKKSLTTNHDFTSPLKQIIMNNLKEYKDSTSPGKLTLSRNFTPTPVPKNKKLYQTSETKSASSFLDTFEGYFDQRKIVRTNAKSRHTMSMAPDVTREEFSLVSNFFNENFQKRPRQKLFEIQKKMFPQYWFELTQGFSLLFYGVGSKRNFLEEFAIDYLSPKIAYSQLAYENELQQNKPVNSIPCLILNGYNPSCNYRDVFKEITDLLVPAELTRSETKYWGNHVILQIQKMIDFYKNQPLDIKLILVVHNLDGPSIRKNTFQTMLSFLSVIRQIAIVASTDHIYAPLLWDNMKAQNYNFVFHDISNFEPSTVESTFQDVMKMGKSDTSSGAEGAKYVLQSLTVNSKKMYKLLIETQMQNMGNLSANTGPKRGTQRTGVELKLFNHLCAADFIASNEIALRSMLREFIEHKMANITKNNSGMEIIWVPYTYAELEKLLKTVLNTL

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Saccharomyces cerevisiae

Entity 3 Entity 3 polymer

Description description	Origin recognition complex subunit 3
Molecular weight formula_weight	72161.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MSDLNQSKKMNVSEFADAQRSHYTVYPSLPQSNKNDKHIPFVKLLSGKESEVNVEKRWELYHQLHSHFHDQVDHIIDNIEADLKAEISDLLYSETTQKRRCFNTIFLLGSDSTTKIELKDESSRYNVLIELTPKESPNVRMMLRRSMYKLYSAADAEEHPTIKYEDINDEDGDFTEQNNDVSYDLSLVENFKRLFGKDLAMVFNFKDVDSINFNTLDNFIILLKSAFKYDHVKISLIFNINTNLSNIEKNLRQSTIRLLKRNYHKLDVSSNKGFKYGNQIFQSFLDTVDGKLNLSDRFVEFILSKMANNTNHNLQLLTKMLDYSLMSYFFQNAFSVFIDPVNVDFLNDDYLKILSRCPTFMFFVEGLIKQHAPADEILSLLTNKNRGLEEFFVEFLVRENPINGHAKFVARFLEEELNITNFNLIELYHNLLIGKLDSYLDRWSACKEYKDRLHFEPIDTIFQELFTLDNRSGLLTQSIFPSYKSNIEDNLLSWEQVLPSLDKENYDTLSGDLDKIMAPVLGQLFKLYREANMTINIYDFYIAFRETLPKEEILNFIRKDPSNTKLLELAETPDAFDKVALILFMQAIFAFENMGLIKFQSTKSYDLVEKCVWRGI

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Saccharomyces cerevisiae

Entity 4 Entity 4 polymer

Description description	Origin recognition complex subunit 4
Molecular weight formula_weight	60772.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MTISEARLSPQVNLLPIKRHSNEEVEETAAILKKRTIDNEKCKDSDPGFGSLQRRLLQQLYGTLPTDEKIIFTYLQDCQQEIDRIIKQSIIQKESHSVILVGPRQSYKTYLLDYELSLLQQSYKEQFITIRLNGFIHSEQTAINGIATQLEQQLQKIHGSEEKIDDTSLETISSGSLTEVFEKILLLLDSTTKTRNEDSGEVDRESITKITVVFIFDEIDTFAGPVRQTLLYNLFDMVEHSRVPVCIFGCTTKLNILEYLEKRVKSRFSQRVIYMPQIQNLDDMVDAVRNLLTVRSEISPWVSQWNETLEKELSDPRSNLNRHIRMNFETFRSLPTLKNSIIPLVATSKNFGSLCTAIKSCSFLDIYNKNQLSNNLTGRLQSLSDLELAILISAARVALRAKDGSFNFNLAYAEYEKMIKAINSRIPTVAPTTNVGTGQSTFSIDNTIKLWLKKDVKNVWENLVQLDFFTEKSAVGLRDNATAAFYASNYQFQGTMIPFDLRSYQMQIILQELRRIIPKSNMYYSWTQL

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Saccharomyces cerevisiae

Entity 5 Entity 5 polymer

Description description	Origin recognition complex subunit 5
Molecular weight formula_weight	55347.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MNVTTPEVAFREYQTNCLASYISADPDITPSNLILQGYSGTGKTYTLKKYFNANPNLHAVWLEPVELVSWKPLLQAIARTVQYKLKTLYPNIPTTDYDPLQVEEPFLLVKTLHNIFVQYESLQEKTCLFLILDGFDSLQDLDAALFNKYIKLNELLPKDSKINIKFIYTMLETSFLQRYSTHCIPTVMFPRYNVDEVSTILVMSRCGELMEDSCLRKRIIEEQITDCTDDQFQNVAANFIHLIVQAFHSYTGNDIFALNDLIDFKWPKYVSRITKENIFEPLALYKSAIKLFLSTDDNLSENGQGESAITTNRDDLENSQTYDLSIISKYLLIASYICSYLEPRYDASIFSRKTRIIQGRAAYGRRKKKEVNPRYLQPSLFAIERLLAIFQAIFPIQGKAESGSLSALREESLMKANIEVFQNLSELHTLKLIATTMNKNIDYLSPKVRWKVNVPWEIIKEISESVHFNISDYFSDIHE

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Saccharomyces cerevisiae

Entity 6 Entity 6 polymer

Description description	Origin recognition complex subunit 6
Molecular weight formula_weight	50369.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MSMQQVQHCVAEVLRLDPQEKPDWSSGYLKKLTNATSILYNTSLNKVMLKQDEEVARCHICAYIASQKMNEKHMPDLCYYIDSIPLEPKKAKHLMNLFRQSLSNSSPMKQFAWTPSPKKNKRSPVKNGGRFTSSDPKELRNQLFGTPTKVRKSQNNDSFVIPELPPMQTNESPSITRRKLAFEEDEDEDEEEPGNDGLSLKSHSNKSITGTRNVDSDEYENHESDPTSEEEPLGVQESRSGRTKQNKAVGKPQSELKTAKALRKRGRIPNSLLVKKYCKMTTEEIIRLCNDFELPREVAYKIVDEYNINASRLVCPWQLVCGLVLNCTFIVFNERRRKDPRIDHFIVSKMCSLMLTSKVDDVIECVKLVKELIIGEKWFRDLQIRYDDFDGIRYDEIIFRKLGSMLQTTNILVTDDQYNIWKKRIEMDLALTEPL

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Saccharomyces cerevisiae

Entity 7 Entity 7 polymer

Description description	72bp-oring DNA, ACS305, T-rich
Molecular weight formula_weight	22203.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	G

TGGTTTTTATATGTTTTGTTATGTATTGTTTATTTTCCCTTTAATTTTAGGATATGAAAACAAGAATTTATC

Entity 8 Entity 8 polymer

Description description	72bp-oring DNA, ACS305, A-rich
Molecular weight formula_weight	22174.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	H

GATAAATTCTTGTTTTCATATCCTAAAATTAAAGGGAAAATAAACAATACATAACAAAACATATAAAAACCA

Entity 9 Entity 9 non-polymer

Description description	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 10 Entity 10 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	5zr1E01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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Resolution resolution	3.00 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	164857

Saccharomyces Cerevisiae Origin Recognition Complex Bound to a 72-bp Origin DNA containing ACS and B1 element

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

Origin recognition complex subunit 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

Origin recognition complex subunit 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

Origin recognition complex subunit 3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Origin recognition complex subunit 4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Origin recognition complex subunit 5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Origin recognition complex subunit 6

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

5zr1__assembly_1__model_1

5zr1__assembly_1__model_1 | I(q)

5zr1__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (10)

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 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer

Entity 8 Entity 8 polymer

Polymer Polymer