SAXSdb — 9yf5

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

30 kDa protein

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 84	Non-contractile tail sheath × 6 （A0MZE7） Gp64 × 6 （A0MZE6） Gp54 × 12 （Q859Q3） 60 kDa protein × 36 （A0MZE8） Probable portal protein × 12 （A0MZE1）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0MZE9_BPN4
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain AA； PDBConstruct 1–236； UniProt 1–236 Author chain AB； PDBConstruct 1–236； UniProt 1–236 Author chain AC； PDBConstruct 1–236； UniProt 1–236 Author chain AD； PDBConstruct 1–236； UniProt 1–236 Author chain AE； PDBConstruct 1–236； UniProt 1–236 Author chain AF； PDBConstruct 1–236； UniProt 1–236 Author chain AG； PDBConstruct 1–236； UniProt 1–236 Author chain AH； PDBConstruct 1–236； UniProt 1–236 Author chain AI； PDBConstruct 1–236； UniProt 1–236 Author chain AJ； PDBConstruct 1–236； UniProt 1–236 Author chain AK； PDBConstruct 1–236； UniProt 1–236 Author chain AL； PDBConstruct 1–236； UniProt 1–236

Non-contractile tail sheath

OrganismNot specified

UniProt A0MZE7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 84	30 kDa protein × 12 （A0MZE9） Gp64 × 6 （A0MZE6） Gp54 × 12 （Q859Q3） 60 kDa protein × 36 （A0MZE8） Probable portal protein × 12 （A0MZE1）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NCTSP_BPN4
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain LA； PDBConstruct 1–1382； UniProt 1–1382 Author chain LB； PDBConstruct 1–1382； UniProt 1–1382 Author chain LC； PDBConstruct 1–1382； UniProt 1–1382 Author chain LD； PDBConstruct 1–1382； UniProt 1–1382 Author chain LE； PDBConstruct 1–1382； UniProt 1–1382 Author chain LF； PDBConstruct 1–1382； UniProt 1–1382

Gp64

OrganismNot specified

UniProt A0MZE6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 84	30 kDa protein × 12 （A0MZE9） Non-contractile tail sheath × 6 （A0MZE7） Gp54 × 12 （Q859Q3） 60 kDa protein × 36 （A0MZE8） Probable portal protein × 12 （A0MZE1）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0MZE6_BPN4
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain SA； PDBConstruct 1–417； UniProt 1–417 Author chain SB； PDBConstruct 1–417； UniProt 1–417 Author chain SC； PDBConstruct 1–417； UniProt 1–417 Author chain SD； PDBConstruct 1–417； UniProt 1–417 Author chain SE； PDBConstruct 1–417； UniProt 1–417 Author chain SF； PDBConstruct 1–417； UniProt 1–417

Gp54

OrganismNot specified

UniProt Q859Q3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 84	30 kDa protein × 12 （A0MZE9） Non-contractile tail sheath × 6 （A0MZE7） Gp64 × 6 （A0MZE6） 60 kDa protein × 36 （A0MZE8） Probable portal protein × 12 （A0MZE1）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q859Q3_BPN4
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain TA； PDBConstruct 1–299； UniProt 1–299 Author chain TB； PDBConstruct 1–299； UniProt 1–299 Author chain TC； PDBConstruct 1–299； UniProt 1–299 Author chain TD； PDBConstruct 1–299； UniProt 1–299 Author chain TE； PDBConstruct 1–299； UniProt 1–299 Author chain TF； PDBConstruct 1–299； UniProt 1–299 Author chain TG； PDBConstruct 1–299； UniProt 1–299 Author chain TH； PDBConstruct 1–299； UniProt 1–299 Author chain TI； PDBConstruct 1–299； UniProt 1–299 Author chain TJ； PDBConstruct 1–299； UniProt 1–299 Author chain TK； PDBConstruct 1–299； UniProt 1–299 Author chain TL； PDBConstruct 1–299； UniProt 1–299

60 kDa protein

OrganismNot specified

UniProt A0MZE8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 84	30 kDa protein × 12 （A0MZE9） Non-contractile tail sheath × 6 （A0MZE7） Gp64 × 6 （A0MZE6） Gp54 × 12 （Q859Q3） Probable portal protein × 12 （A0MZE1）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0MZE8_BPN4
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain XA； PDBConstruct 1–556； UniProt 1–556 Author chain XB； PDBConstruct 1–556； UniProt 1–556 Author chain XC； PDBConstruct 1–556； UniProt 1–556 Author chain XD； PDBConstruct 1–556； UniProt 1–556 Author chain XE； PDBConstruct 1–556； UniProt 1–556 Author chain XF； PDBConstruct 1–556； UniProt 1–556 Author chain XG； PDBConstruct 1–556； UniProt 1–556 Author chain XH； PDBConstruct 1–556； UniProt 1–556 Author chain XI； PDBConstruct 1–556； UniProt 1–556 Author chain XJ； PDBConstruct 1–556； UniProt 1–556 Author chain XK； PDBConstruct 1–556； UniProt 1–556 Author chain XL； PDBConstruct 1–556； UniProt 1–556 Author chain YA； PDBConstruct 1–556； UniProt 1–556 Author chain YB； PDBConstruct 1–556； UniProt 1–556 Author chain YC； PDBConstruct 1–556； UniProt 1–556 Author chain YD； PDBConstruct 1–556； UniProt 1–556 Author chain YE； PDBConstruct 1–556； UniProt 1–556 Author chain YF； PDBConstruct 1–556； UniProt 1–556 Author chain YG； PDBConstruct 1–556； UniProt 1–556 Author chain YH； PDBConstruct 1–556； UniProt 1–556 Author chain YI； PDBConstruct 1–556； UniProt 1–556 Author chain YJ； PDBConstruct 1–556； UniProt 1–556 Author chain YK； PDBConstruct 1–556； UniProt 1–556 Author chain YL； PDBConstruct 1–556； UniProt 1–556 Author chain ZA； PDBConstruct 1–556； UniProt 1–556 Author chain ZB； PDBConstruct 1–556； UniProt 1–556 Author chain ZC； PDBConstruct 1–556； UniProt 1–556 Author chain ZD； PDBConstruct 1–556； UniProt 1–556 Author chain ZE； PDBConstruct 1–556； UniProt 1–556 Author chain ZF； PDBConstruct 1–556； UniProt 1–556 Author chain ZG； PDBConstruct 1–556； UniProt 1–556 Author chain ZH； PDBConstruct 1–556； UniProt 1–556 Author chain ZI； PDBConstruct 1–556； UniProt 1–556 Author chain ZJ； PDBConstruct 1–556； UniProt 1–556 Author chain ZK； PDBConstruct 1–556； UniProt 1–556 Author chain ZL； PDBConstruct 1–556； UniProt 1–556

Probable portal protein

OrganismNot specified

UniProt A0MZE1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 84	30 kDa protein × 12 （A0MZE9） Non-contractile tail sheath × 6 （A0MZE7） Gp64 × 6 （A0MZE6） Gp54 × 12 （Q859Q3） 60 kDa protein × 36 （A0MZE8）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PORTL_BPN4
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain PA； PDBConstruct 1–763； UniProt 1–763 Author chain PB； PDBConstruct 1–763； UniProt 1–763 Author chain PC； PDBConstruct 1–763； UniProt 1–763 Author chain PD； PDBConstruct 1–763； UniProt 1–763 Author chain PE； PDBConstruct 1–763； UniProt 1–763 Author chain PF； PDBConstruct 1–763； UniProt 1–763 Author chain PG； PDBConstruct 1–763； UniProt 1–763 Author chain PH； PDBConstruct 1–763； UniProt 1–763 Author chain PI； PDBConstruct 1–763； UniProt 1–763 Author chain PJ； PDBConstruct 1–763； UniProt 1–763 Author chain PK； PDBConstruct 1–763； UniProt 1–763 Author chain PL； PDBConstruct 1–763； UniProt 1–763

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	9yf5
Deposition date deposition_date	2025-09-25
Structure title title	N4 Empty Particle C6 Tail
Keywords keywords	dodecamer, bacteriophage portal, VIRAL PROTEIN; VIRAL PROTEIN
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.

9yf5__assembly_1__model_1

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

Download this curve (.dat)

9yf5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9yf5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	0.00 Å
Rg (electron density)	119.40 Å
Total Rg	119.20 Å
Atom count	207084
Residues	26124
Excluded volume	3681100 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9yf5__assembly_1__model_1`	84-meric （84）	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	30 kDa protein
Molecular weight formula_weight	27192.4 kDa
Source method src_method	nat
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	AA,AB,AC,AD,AE,AF,AG,AH,AI,AJ,AK,AL
Atom count atom_count	207084

MYYIEELFCRLANGVLNNTGIVTDDRGDIEDDSKPFIIVAANEALTRLHGRFNMRNNNVVVEMQEGRTNYPLLAKYAVQSYDPNEVKCPFIMDLAGEKFAEDVIRILEVYDDKGRRRPLNDRNNPCSLFTPRPNVLQNNAPKAWEVLNVMYQAKHPKLSTAEDGYNEIDIPDTLDPALDAYIAYRYYTSLNTPESSAKAAEYLSFYDSICREVVEYDLTSDTEVDTNTLFRKRGWR

Entity 2 Entity 2 polymer

Description description	Non-contractile tail sheath
Molecular weight formula_weight	154255.1 kDa
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	LA,LB,LC,LD,LE,LF

MSIEDYLKGKNCLASPNYDPDDQHSSWREDLPQFKKDREHLTLVNTRRNRTYNTKLNRFDPEYWVVDYNALMVATIIPYGSKSFKVPCQWRTNKDFLGVRWMTEDTFDHHLYRYETDPNYLGLILAFRHNPDEPDKFTVTIQTPEKAYTYRLAPYGFNNKTRRWECLDTKYGTKRTYQADIFVATDEDIPESEMTEVYGTKDYIFILDFADLRTGVAFNGVTINPRNITMISFDCTEAHHGLGKDAYIAAMYNNDDGATFQMEIGGIHTNAALAAGDKLQCIWRYLDVNGNAQAAENEFEVVSYEGFGTSNFSVKCKGMLPGKFIGCDAFYGKYLQTDGPIKQVDSVKWFTNLTVSGSGRKQLGQRKYPQVVMGMGMTSGFDDGYNLTPERQVKMAYGLGYRDWWTTYIGMSHYWKGLTAFQDKETGELITEQTVLDYPILFAGESQVAIHFMSGAYPDRGYDVFQKYMTETWGINYAGVHPINGTTGSTAVDRACAVNPNSEVFDPTQSSGAGGLWWWDLEADKPGPALLHCVGQVGKLKPKAIIWGQGDQDATALAYPGDRNPAPSLTRTKQATKKVFEYLRSLYGQIPIFIQELSYAWGITNTDAPNVPIRTGLPSFLAARRNTWGDIEFRWKSYGLDPALAQYRIEIYNPSNLNQILHSFVVSGTQEANGYVYADFTVEDWIPVMMEAVGSPNPWEFMKWRVVCLYQEREIPSAPWSDNIPLDNAGLVKKTILVGINQFGGGHFTDMSDPTATTANGAIGRKDKVSASTLRLTFAEKAGLRPIQVMPVNVAADSAGMTVGTHKWWNTSSNSPGDALLAINDMVKGLGVKPDYFIEANPWETMYMKDVNSSTWPALMTAFESSNKAMLAWMRTNWGNPNLEIWFQGATTVWFGVAPPNDLNSEATVTVRDKQIQMATANIGFKLGSFVPGSNLYTAYRNVESSWIYYTVEAFHATAIELGEALALNINRATNPPDWSYLRPPANLQGRKLATRDIKMTWDNRAGITHWKYANRHVTTGAEISSGILTSPEYVFTLNDQQNAYNGDTLNMSFSVSEYAADSGAVGASSSFVGVVQNGSYMQTPTQLKAAKQLNGDIIFTWVGRPSWQHFWVVNTSVNDSKTVIFSKEWSSESLTWTVAEQNEFYGLEEGGATHVIFMVSEYDPSNGLVSIGAQVTGQAEQPSNPMNPVAGLYAVFTGDPGNSNIKIMWDKPSVGGRDVRIRNMHVTSSATISDQFVSDNNLVFTREEQVAAYGFTASSVSVRAQEHDIESGALGLTTEYVAVPETAGTVGQGFAKKDSVGNCTMSWEVGDAVQWQVEILNAENSTVVKTEIVVAPTITWMAEEITAEYGYLTDHMVWRVRPYRADGASNVAKQFDMTATL

Entity 3 Entity 3 polymer

Description description	Gp64
Molecular weight formula_weight	48100.7 kDa
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	SA,SB,SC,SD,SE,SF

MSNAAVVPMPYSPTTVPREQIREIQLQLINEMTDVHMGALTAQYMPDDFTFEPGIGQIHFNVETSRKVCLDLAKSVLRLVPVYPLVSPVKKQHDDYWFVGRLGLDPVSEPEPINMPTMEFYKRFLSLLHERDMKFVNSVAYEILNFFMPDEWKQLNWKGDPALSGWYPPSSFIQPTNKDALDFVSKAQCQILKECQNLGMELYFQIGEPWWWDGSYNTGEGKNAPCIYDPKTMALYKEETGNDVPTPWIKDIFAPVEEHQWPYVDWLCTKLGQSTNYIRDYVKGKFPDAQATLLFFTPQIMSPASELTGRLNFPESEWIFPNYDFVQIEDYDWIIDGRLDLVPLTFDAAVNRLGYPLNVVHYFIGFVLLPEDAKKIWADVDKAWGLALEAGIPHIYPWSYTQVMRDGVIYAVPKVCG

Entity 4 Entity 4 polymer

Description description	Gp54
Molecular weight formula_weight	32438.4 kDa
Source method src_method	nat
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	TA,TB,TC,TD,TE,TF,TG,TH,TI,TJ,TK,TL

MSCGAELEANALLTALVAGEDFTLPDIDMSGSEYDIPGGINSPIYAEIEKITTEQLTTREVGGSGVFDALMQSASNHLLAEFKNNRITGGDYVKAYIATMEACMANAVQFLTTKDQAYWNAVTAQVAAITARANLGIIKANFVTAKIQALATKAEYALTKLKLSNESVTYCTAQYNLSSMLPQQLLMLKNQTTQVAEQTKLTTEQINMTKEQKEAQRAQTSDTRTDGTRVAGSVGKQKELYDQQITSYKRDAEVKAAKLFTDAWVTQKTIDEGLSPPNGFTNSSLDSILTALKNNNALG

Entity 5 Entity 5 polymer

Description description	60 kDa protein
Molecular weight formula_weight	58943.9 kDa
Source method src_method	nat
Copy count entity_count	36

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	XA,XB,YA,YB,ZA,ZB,XC,XD,YC,YD,ZC,ZD,XE,XF,YE,YF,ZE,ZF,XG,XH,YG,YH,ZG,ZH,XI,XJ,YI,YJ,ZI,ZJ,XK,XL,YK,YL,ZK,ZL

MSGHTPFNTIPNEGYCCETLNDPIVDKMIGNAYYVVKFVALRMPFIKNVSDNMTQLLAIHNKLTELSAIYTKLDELQLIHNNLDKLQELYNQLSKLTGLYDNLQALLRVYDNLTPINTVASNIDAVNTVATDIAKVIIVSAQIDKVITVANSITNVNTVAGSIDAVNTVSTNINAIKNVNTNMAALLDLDNHMTELLAVHARLGDLVTIAEQLDTIIADHEKYATAEGAGLIGFNQAQTYAANTVGAMLRQVITMGNDKGGYAVAGKLTSARGVWSLATGSINMNAPTAGAVANLVLNYKAGKVSGLLVAPSQQMALDGLIMGASTADNTATVSVTAPLRFKADLTAKTISGVNTRIMPSSAVTLNVDAYGGITLGYPPSLQTVEPVMTFITPTGKAPLTPRFSSVTAGAAVLVMVGEAEAQLKYSGGGWAAVSDWDSGTYCAFDTVSGELTVYHSTLIKDSTVTFSLLLPTDDTQLTAQLKSHTDSSFVVKIAKPDGSLLDAPLEGMGIMYSRGMHGIYKVPYGSLIVDVGRVQVKFSEFNTTEGISVVGINSNA

Entity 6 Entity 6 polymer

Description description	Probable portal protein
Molecular weight formula_weight	85642.5 kDa
Source method src_method	nat
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	PA,PB,PC,PD,PE,PF,PG,PH,PI,PJ,PK,PL

MEQNTDSMVPLPDPSQATKLTSWKNELSLQALKADLDAAKPSHTAMMIKVKEWNDLMRIEGKAKPPKVKGRSQVQPKLVRRQAEWRYSALTEPFLGSNKLFKVTPVTWEDVQGARQNELVLNYQFRTKLNRVSFIDNYVRSVVDDGTGIVRVGWNREIRKEKQEVPVFSLFPIQTQEQADALQQALQLRTDNPRGYEENVDEAIKESVRFFDETGQATYAVQTGTTTTEVEVPLANHPTVEMLNPENIIIDPSCQGDINKAMFAIVSFETCKADLLKEKDRYHNLNKIDWQSSAPVNEPDHATTTPQEFQISDPMRKRVVAYEYWGFWDIEGNGVLEPIVATWIGSTLIRLEKNPYPDGKLPFVLIPYMPVKRDMYGEPDAELLGDNQAVLGAVMRGMIDLLGRSANGQRGMPKGMLDALNSRRYREGEDYEYNPTQNPAQMIIEHKFPELPQSALTMATLQNQEAESLTGVKAFAGGVTGESYGDVAAGIRGVLDAASKREMAILRRLAKGMSEIGNKIIAMNAVFLAEHEVVRITNEEFVTIKREDLKGNFDLEVDISTAEVDNQKSQDLGFMLQTIGPNVDQQITLNILAEIADLKRMPKLAHDLRTWQPQPDPVQEQLKQLAVEKAQLENEELRSKIRLNDAQAQKAMAERDNKNLDYLEQESGTKHARDLEKMKAQSQGNQQLEITKALTKPRKEGELPPNLSAAIGYNALTNGEDTGIQSVSERDIAAEANPAYSLGSSQFDPTRDPALNPGIRLGN

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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	3.65 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	10265

N4 Empty Particle C6 Tail

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

30 kDa 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

Non-contractile tail sheath

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Gp64

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Gp54

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

60 kDa 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

Probable portal 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

9yf5__assembly_1__model_1

9yf5__assembly_1__model_1 | I(q)

9yf5__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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

7. Citations (1)